Developing highly efficient photocatalysts for the removal of antibiotics and heavy metals is of vital importance but remains a great challenge. In this investigation, a novel S-scheme Cs3PMo12O40/MnIn2S4 (CPM/MIS) heterojunction with core-shell structure was fabricated successfully via hydrothermal synthesis/dissolution-precipitation approaches, which was labelled as x CPM/MIS (x = 5, 7, 9 and 11, respectively). In the composites, these 2D MIS nanoflakes were securely and uniformly affixed on the exterior of 3D CPM nanospheres, which was verified through SEM and TEM. These as-produced materials manifested enhanced photocatalytic activity towards antibiotics (tetracycline (TC) and ciprofloxacin (CIP)) degradation and Cr(VI) reduction with visible light, and the removal rates of the optimal 9 CPM/MIS for TC, CIP and Cr(VI) could reach 97.81%, 61.78% and 67.07%, respectively. Of note, these resulting CPM/MIS composites possessed excellent stability and reusability. The outstanding photocatalytic property was attributed to the synergistic effect arising from the advantageous core-shell structure and S-scheme heterostructure. This configuration strengthened robustly interfacial interaction between the constituents, which effectively enhanced light absorption in visible region, promoted the separation and transfer efficiency of photoinduced carriers, and preserved the charge carriers with heightened redox abilities. The ESR spectra and trapping tests confirmed the dominating role of holes and superoxide radical in contaminants removal. Additionally, the high-performance liquid chromatography-mass spectrometry (HPLC-MS) technique was employed to identify the photodegradation pathways of TC. And the product toxicity was evaluated using QSAR prediction. Conclusively, combining the in situ XPS data and analysis of energy band structure, a S-scheme catalytic mechanism was elucidated. This study opens new avenues for systematically designing and fabricating S-scheme heterojunction photocatalysts with outstanding catalytic property for contaminants removal.