Materials with the ABO3 perovskite structure possess a wide variety of properties including superconductivity, ferroelectric, and magnetic properties. These properties are highly tunable due to the fact that the B site cation can assume multiple valence states and its high structural stability allows for large scale doping and strain. Due to a reduced dimensionality, two dimensional thin films and superlattices grown using techniques such as pulsed laser deposition (PLD) often possess novel properties which differ from the bulk perovskite materials. The origins of these novel properties can be traced to interfacial chemical intermixing, electronic reconstruction, strain as well as defect formation, which cause significant changes in the electronic structures. Therefore, it is crucially important to investigate the atomic and electronic structures of the functional materials in order to understand the correlation between microstructures and physical properties. Chemically-sensitive Z-contrast imaging and bonding-sensitive electron energy loss spectroscopy (EELS) in aberration corrected scanning transmission electron microscopes (STEM) can directly characterize the local structure, strain, composition and bonding on the atomic scale. Determination of the atomic and electronic structures of the interfaces and defects in the thin films can then be correlated with the magnetic and transport properties. Therefore, the understanding of the structure-property relationship for several different systems of perovskite oxide thin films and superlattices were developed on the atomic scale. Multifunctional superlattices composed of ferromagnetic (FM) La(0.7)Sr(0.3)MnO3 (LSMO) and antiferromagnetic (AFM) La(0.7)Sr(0.3)FeO3 (LSFO) have potential applications for next generation data storage and logic devices. Defect formation, driven by strain relaxation in the LSMO/LSFO superlattices can modify not only the structure and surface sharpness, but also the functional properties of the superlattice. Stacking faults were found as one efficient way of strain relaxation while maintaining robust antiferromagnetic properties for a thin [3LSMO][6LSFO] superlattice (repeating motif composed of 3 unit-cell LSMO sublayer and 6 unit-cell LSFO sublayer). On the other hand, for a fully strained [3LSMO][6LSFO], large inter-diffusion across the interface between the LSMO and LSFO layers was detected in EELS line scans, resulting in deteriorated AFM properties. When a [6LSMO][6LSFO] superlattice with one micron thickness, a high density of nanoflowers and cracks/pinholes were observed to result from strain relaxation. The formation of these nanoflowers and cracks/pinholes was suppressed by increasing the growth rate and thereby reducing the growth time and overall thermal treatment of the sample. Strain relaxation was shown to be directly related to the growth conditions and have a large effect on both the structure and functional properties of the superlattices. A series of superlattices composed of non-magnetic La(0.5)Sr(0.5)TiO3 (LSTO) and ferromagnetic LSMO were grown on single crystal oxide substrates with different amounts of misfit strain. No significant electronic structure changes along the interfaces was observed in this series of superlattices as revealed by atomic resolution EELS. In comparison, charge transfer effect was reported for the LSMO/STO superlattices and was shown to cause an ultrathin magnetic dead layer along the interfaces. Thus, compared with the LSMO/STO superlattice, composition tuning of the sublayers was proven to be efficient in controlling the interfacial charge transfer effects in a superlattice. In addition, tetragonal distortion was found to reduce the ferromagnetic ordering, decrease the Tc, increase the resistivity, and even lead to metal-insulator transitions of the superlattices. The strain relaxation defects such as dislocations and low angle grain boundaries serve as important pinning sites for magnetic domains, leading to enhanced coercive field strength. In order to determine the properties of an intermixed interface layer, we have performed a detailed study of the solid solution between LSMO and LSFO, i.e. La(0.7)Sr(0.3)Mn(0.5)Fe(0.5)O3 (LSMFO). A large target-substrate distance during the PLD growth led to cation segregation in the LSMFO film. Cation segregation could cause the formation of diverse local magnetic ordering and B site valence states due to the different local stoichiometry and coordination environment. For the cation segregated LSFMO films, robust ferromagnetic and antiferromagnetic coupling was observed at 150K and room temperature. Decreasing the target-substrate distance resulted to a homogeneous cation distribution in the film, without any ferromagnetic ordering as expected. This result suggests the important role of target-substrate distance and the kinetic energy of the plume species on the crystalline quality and functional properties of perovskite oxide thin films. La(x)Sr(1-x)TiO3 possesses a wide range of functional properties which make it an attractive candidate material for applications such as the conductive buffer for high temperature superconductor growth, transparent conductors, and anodes in solid oxide fuel cells. La(0.5)Sr(0.5)TiO3 thin films were grown using PLD and the resistivity was found to be highly dependent on the O2 background pressure used in the deposition. However, a thin film which was deposited as a single phase film was transformed into a semi-ordered superlattice with TiO2 rich stacking faults and distorted lattices upon exposure to high oxygen pressure (~200torr) during the cooling procedure after deposition. This phase change stabilized Ti4+ ions and dramatically increased the resistivity of the film. In addition, a two dimensional free electron gas could be constructed by confining a few unit cells of La doped STO with STO spacer layers. Our study showed that charge transfer over a distance of ~2 u.c. was present in Sr(0.75)La(0.25)TiO3/STO superlattices. This thickness defined the lower limit for the thickness of the STO spacers in order to confine the charge carriers into two dimensions; secondly, the La dopants were shown to be less localized in thicker superlattice (~100nm) due to interdiffusion upon extended thermal exposure. This information provided important feedback on the fabrication and utilization of this material.In conclusion, several perovskite thin film systems with fascinating properties have been explored in this thesis. Strain states and strain relaxations, defect formation, interfacial atomic mixing, charge transfer, and cation segregation were shown to have profound effect on the functional properties of complex oxide thin film systems. Atomic resolution Z-contrast imaging and EELS provide extremely useful information on the structural and electronic structure variations, which enable us to see the whole picture of growth, structure and properties' interactions.