Heteroepitaxial oxide-based nanocomposite films possessing a variety of functional properties have attracted tremendous research interest. Here, self-assembled vertically aligned nanocomposite (Pr0.5Ba0.5MnO3)1-x:(CeO2)x (x = 0.2 and 0.5) films have been successfully grown on single-crystalline (001) (La,Sr)(Al,Ta)O3 substrates by the pulsed laser deposition technique. Self-assembling behavior of the nanocomposite films and atomic-scale interface structure between Pr0.5Ba0.5MnO3 matrix and CeO2 nanopillars have been investigated by advanced electron microscopy techniques. Two different orientation relationships, (001)[100]Pr0.5Ba0.5MnO3//(001)[1-10]CeO2 and (001)[100]Pr0.5Ba0.5MnO3//(110)[1-10]CeO2, form between Pr0.5Ba0.5MnO3 and CeO2 in the (Pr0.5Ba0.5MnO3)0.8:(CeO2)0.2 film along the film growth direction, which is essentially different from vertically aligned nanocomposite (Pr0.5Ba0.5MnO3)0.5:(CeO2)0.5 films having only (001)[100]Pr0.5Ba0.5MnO3//(001)[1-10]CeO2 orientation relationship. Both coherent and semi-coherent Pr0.5Ba0.5MnO3/CeO2 interface appear in the films. In contrast to semi-coherent interface with regular distribution of interfacial dislocations, interface reconstruction occurs at the coherent Pr0.5Ba0.5MnO3/CeO2 interface. Our findings indicate that epitaxial strain imposed by the concentration of CeO2 in the nanocomposite films affects the self-assembling behavior of the vertically aligned nanocomposite (Pr0.5Ba0.5MnO3)1-x:(CeO2)x films.