Nanorods are a very effective pinning center in YBa2Cu3O7 films, and the vortex pinning mechanism should be understood to further improve the critical current density (J
c) in the nanocomposite films. Matrix defects are naturally formed during nanocomposite growth, and in this study the effect of matrix defects on the J
c in the YBa2Cu3O7 films containing nanorods is discussed. YBa2Cu3O7 + BaHfO3 and YBa2Cu3O7 + BaSnO3 films were prepared by varying the laser repetition frequency to control the matrix defects. All the films contained the nanorods. The YBa2Cu3O7 + BaHfO3 film of 2 Hz exhibits high J
c for magnetic field parallel to the c-axis (B//c) due to the nanorods and the isolated random point defects. In the YBa2Cu3O7 + BaHfO3 film of 10 Hz, while the short stacking faults and networked random point defects decreased the J
c for B//c, the short stacking faults improved the J
c for tilted magnetic field. In the YBa2Cu3O7 + BaSnO3 film of 10 Hz, the isolated random point defects improved J
c regardless of the magnetic field direction. While the ab-plane correlated defects are analyzed by the structural observation, the network or isolated nature of the random point defects can be discussed by the normal state resistivity. The matrix defects of YBa2Cu3O7 nanocomposite films should be designed considering the correlated/network/isolated nature which is determined by the morphology and defect concentration.