To explore the interface effects on enhancing critical current density in YBa 2 Cu 3 O 7−δ (YBCO) thin films, four heterogeneous systems, of which two have small opposite lattice misfits (i.e., the YBCO/STO (∼1.6%) and the YBCO/LAO (∼−1.6%)), and the other two have relatively large opposite mismatch (i.e., the YBCO/MgO (∼8.9%) and the YBCO/YSZ (∼−5.9%)), were selected and synthesized by pulsed-laser deposition. A detailed microstructure analysis including XRD, TEM and the state-of-the-art Cs-corrected STEM imaging, and a thorough superconducting property characterization including critical transition temperature (T c ) and critical current density (J self-field c and J in-field c (H c) at various temperatures), were conducted for all four heterogeneous systems. The results reveal that the YBCO intrinsic defects, driven by the interface mismatch of different strain states, present a diverse nature in their distribution and density, and thus different flux-pinning performances under various measurement conditions. This study provides an in-depth insight into the microstructure-property correlation in a strongly correlated electronic system, the YBCO heterogeneous structures.