Enzyme-Photo-coupled Catalytic System (EPCS) integrates the light absorption capacity of photocatalysts and the high activity/specificity of enzymes, which is becoming an emerging technology platform to mimic natural photosynthesis for harnessing solar energy to generate valuable products, including bulk chemicals, energy chemicals and pharmaceutical chemicals. Cofactors including NAD(P)+/NAD(P)H, as “energy currency”, are involved in over 80% biocatalytic redox reactions, establishing a bridge of mass/energy exchange between photocatalysis and cofactor–dependent enzyme catalysis. Although numerous efforts have been devoted, the performance of current EPCS is far from the theoretical upper limit. The individual and synergistic intensification of molecule-electron-proton transfer evolves a critical yet challenging issue in EPCS. This Review will focus on the molecule-electron-proton transfer in natural photosynthesis and in EPCS. Future endeavors to intensify all three transfers to construct a more efficient EPCS are suggested as pursuit for a new pattern of modern chemical engineering.