Self-organized nanorods in YBa2Cu3O7−δ films are important pinning centers from the technical and fundamental views. While influence of nanoscale factors (>4–5 nm) on the vortex pinning has already been discussed in detail, the interface control of nanorods (at the smaller scale) has not yet been performed. Here, it is demonstrated that the stacking faults can control the nanorod interface to improve the vortex pinning. The stacking faults were formed across the nanorods by post-annealing the YBa2Cu3O7−δ films containing BaMO3 (M = Zr, Sn, Hf) nanorods. The strong bonding between YBa2Cu3O7−δ and BaMO3 varies the atomic position of YBa2Cu3O7−δ, degrading an interface sharpness and an elementary pinning force of the nanorod. Scanning transmission electron microscopy and density functional theory calculation clarified that the stacking faults broke the strong bonding between YBa2Cu3O7−δ and BaMO3 at the nanorod interface, and reduced the local strain around the nanorods, improving the elementary pinning force. As a result, the critical current density was improved in low temperature and low magnetic field when magnetic field was aligned with the c-axis. Thus, the combined effect of nanoinclusions and crystalline defects, in the present case, nanorods and stacking faults, can control the interface of nanoinclusion pinning centers, opening the interface design to realize the ideal pinning situation.