Intriguing properties of self-organized nano composites of perovskite oxides are usually derived from the complex interface of constituent material phases. A sophisticated control of such a system is required for a broad range of energy and device applications, which demand a comprehensive understanding of the interface at the atomic scale. Here, we visualized and theoretically modeled the highly elastically strained nanorod, the interface region with misfit dislocations and heterointerface distortion, and the matrix with strain-induced oxygen vacancies in the self-organized YBa2Cu3O7_(delta) nanocomposite films with Ba perovskite nanorods. Large misfit strain was elastically accommodated in the nanocomposites, but since the elastic strain was mainly accommodated by the nanorods, the concentration of strain-induced oxygen vacancies was small enough for the matrix to keep high critical temperature (>85 K). The interfacial bonding distorted the atomic structure of YBa2Cu3O7_(delta), but the thickness of distortion was limited to a few unit cells (less than the coherence length) due to the electron screening. The effect of volume fraction on elastic strain and the electron screening are crucial for strong vortex pinning without significant degradation of both the elementary pinning force and critical temperature in the nanocomposites. Thus, we comprehensively clarified the self-organized nanocomposite structure for on-demand control of superconductivity and oxide functionality in the nanocomposite engineering of perovskite oxides.