The development of biotic-abiotic photosynthetic systems is becoming one of the most promising strategies towards the thirsty demand for sustainable energy production. However, considerable efforts are still required to further optimize the design and avoid the utilization of high-value substances while achieving highly efficient hydrogen production. Here we show a way to construct an Escherichia coli (E. coli)-quantum dots hybrid system by expressing ferredoxin (Fd), Fd-NAD(P)+ reductase (FNR), and [FeFe]-hydrogenase ([FeFe]H2ase) as a potential biocatalyst. We reveal that electrons originating from the quantum dots could be redirected through the newly established electron transport chain NADH/NAD+-FNR-Fd to [FeFe]H2ase, which contributes a key mechanism to boost the highest H2 production activity (3149.5 μmol gdcw−1h−1) by only using glycerol as the carbon source. Our work sheds light on the advantages of an intracellular biological hybrid system by combining the photocatalytic capacity with the optimized metabolic power to produce biofuels.