Herein, we report the preparation of AgVO3 nanoparticles-decorated multi-shelled ZnO microspheres 0D/3D Z-scheme heterojunction photocatalysts via calcination of carbon sphere template and in situ growth method. The prepared ZnO/AgVO3 composites showed enhanced photocatalytic performance for photodegradation of ciprofloxacin (CIP) and photocatalytic reduction of Cr(VI) compared to the single-phase photocatalysts under the same irradiation conditions. Noticeably, the photocatalytic removal rate of CIP and Cr(VI) reached 90% at 90 min and 45 min, respectively, for the ZnO/AgVO3 composite with an optimal AgVO3 content. The photocatalytic removal rate for CIP and Cr(VI) was, respectively, about 2.43-fold and 4.84-fold as high as that of the pure ZnO. Furthermore, a reasonable degradation pathway for CIP has been proposed based on LC-MS results. The enhanced photocatalytic performance could be attributed to the extended visible-light absorption, promoted separation and transportation efficiency of the photogenerated electron-hole pairs. Significantly, the Z-scheme heterojunction was verified according to radical capture experiments and theoretical calculations based on the density functional theory (DTF) framework. We believe this work will give an innovative view for constructing multi-shelled 0D/3D photocatalytic systems for eliminating environmental pollutants and enhancing environmental remediation.