Metal nanoparticle exsolution from metal oxide hosts has recently garnered great attention to improve the performance of energy conversion and storage devices. In this study, the nickel exsolution mechanisms in a vertically aligned nanostructure (VAN) thin film of heteroepitaxial (Sr0.9Pr0.1)0.9Ti0.9Ni0.1O3−δ-Ce0.9Gd0.1O1.95 with a columnar architecture was investigated for the first time. Experimental results and Density Functional Theory (DFT) calculations reveal that the multiple vertical interphases in a VAN with a hierarchical arrangement provide faster and more selective Ni diffusion pathways to the surface than traditional bulk diffusion in epitaxial films. Kinetic studies conducted at different temperatures and times indicate that the nucleation process of the exsolved metal nanoparticles primarily takes place at the surface through the phase boundaries of the columns. The vertical strain is crucial in preserving the film’s microstructure, yielding a robust heteroepitaxial architecture after reduction. This innovative heteromaterial opens up new possibilities for designing efficient devices through advanced structural engineering to achieve controlled nanoparticle formation.