Magic-sized nanoclusters (MSCs) have recently deemed as a novel and crucial sector of nanomaterials on account of their large absorption coefficient for light harvesting, peculiar quantum confinement effect, and abundant active. Nevertheless, precise control of photoinduced charge carriers over MSCs has so far not yet been reported because of the ultra-short carrier lifetime and intrinsic instability of MSCs, which renders the complexity of MSCs photosystems with photoredox mechanism remaining blank. Herein, we for the first time conceptually demonstrate the grafting of amino-containing organic molecular onto the L-cysteine (L-Cys) ligand of CdSe@L-Cys MSCs as charge transport mediator, and the amino functional group acts as an efficient electron-withdrawing trap, which markedly boosts the charge separation and prolongs the charge lifetime of CdSe@L-Cys MSCs, resulting in the significantly improved photocatalytic hydrogen generation performances under visible light irradiation along with favorable stability. Our work will provide sparking ideas for fine tuning of photoinduced charge separation and transfer over transition metal chalcogenides MSCs photosystems for solar-to-hydrogen energy conversion.