Photocatalytic degradation is a promising method for controlling the increasing contamination of the water environment due to pharmacologically active compounds (PHACs). Herein, oxygen vacancy (OV)-modulated Z-scheme CuWO4/CuBi2O4 hybrid systems were fabricated via thermal treatment by loading of CuWO4 nanoparticles with OVs on CuBi2O4 surfaces. The synthesized CuWO4/CuBi2O4 hybrid samples exhibited an enhanced photodegradation ability to remove PHACs under visible-light irradiation. More importantly, an optimized sample (10 wt % CuWO4/CuBi2O4) exhibited superior catalytic activity and excellent recycling stability for PHAC photodegradation. In addition, possible degradation paths for PHAC removal over the CuWO4/CuBi2O4 hybrid systems were proposed. The enhanced photocatalytic performance could be attributed to the efficient separation and transfer of photoformed charge pairs via the Z-scheme mechanism. This Z-scheme mechanism was systematically analyzed using trapping experiments of active species, ultraviolet photoelectron spectroscopy, electron spin resonance, and the photodepositions of noble metals. The findings of this study can pave the way for developing highly efficient Z-scheme photocatalytic systems for PHAC photodegradation.