Biohydrogen is a clean and renewable energy, but the low yield caused by the lack of reducing power in cells greatly restricts the industrialization of biohydrogen production. Photobiohybrid systems (PBSs) can integrate the high light energy utilization efficiency of photocatalysts with the excellent catalytic performance of microorganisms. Here, gold nanoparticles were targeted into Clostridium butyricum as intracellular photosensitizers to construct a PBS that could efficiently produce biohydrogen under visible light, with the apparent quantum yield as high as 19.31%. Compared with the dark-fermented C. butyricum, the biohydrogen production of PBS increased by 88.74%. The mechanism of photoelectrons from Au NPs to C. butyricum was elucidated by the transcriptome. Compared with the darkfermented biohybrids, the expressions of biohydrogen generation-related enzymes, such as hydrogenase and pyruvate formate lyase genes, in the PBS were all upregulated more than 2 times. Furthermore, the genes of riboflavin synthase, electron transfer flavoprotein (ETF), and FAD-dependent oxidoreductase, which are closely related to electron transformation, were all significantly upregulated. The photoelectrons were transferred to the hydrogenase via ETF and FAD 2+ to enhance biohydrogen production, independent of pyruvate decomposition. This PBS provides theoretical guidance for constructing an efficient light-driven microbial manufacturing system.