Fabrication of a S-scheme heterojunction with staggered energy band structures can accelerate the charge separation and retain high redox potentials. Herein, a series of x wt% H3PMo12O40/MgIn2S4 (abbr. x% PMo12/MIS; x = 7.5, 10.0, 12.5, 15.0 and 17.5) S-scheme heterojunctions were successfully constructed by a hydrothermal technology and exhibited efficient and durable visible-light-driven photocatalytic properties of H2-evolution and formaldehyde (HCHO) degradation. Particularly, the 12.5 % PMo12/MIS sample represented the optimal H2 evolution rate of 232.53 μmol·g−1·h−1 with the apparent quantum efficiency (AQE) value of 1.52 % (λ = 420 nm), and HCHO removal rate of 64.20 % in 60 min. Moreover, the intermediate products formed during the removal process of HCHO were revealed through in situ DRIFTS method. The superior photocatalytic activities mainly stemmed from the enhanced absorption of visible light, and effective separation of photoinduced charge carriers. Furthermore, the S-scheme photocatalytic mechanism for PMo12/MIS system was confirmed via in situ irradiated X-ray photoelectron spectroscopy, radical capturing tests and electron spin resonance data, and semiconductor energy band theory. The current study affords a valuable perspective for fabricating highly efficient S-scheme heterojunction photocatalysts for hydrogen evolution and HCHO elimination.