The native cysteine (Cys)-Ag-3 cluster hydrogel is approved for the first time by both experimental and theoretical studies. From the detailed molecular structure and energy information, three factors are found to ensure the self-assembly of Cys and Ag-3, and result in the hydrogel. First, the Ag-S bonds make Cys and Ag-3 form Cys-Ag-3-Cys monomer. Second, intermolecular hydrogen bonds between carboxyl groups of adjacent monomer push them self-assembled. Third, more monomer precisely self-assemble to produce the -[Cys-Ag-3-Cys](n) multimer, e.g., a single molecular chain with the left-handed helix conformation, via a benign thermodynamic process. These multimers entangle together to form micro-network to trap water and produce hydorgel in situ. The hydrogen bonds of hydrogel are sensitive to thermal and proton stimuli, and the hydrogel presents lysosome targeting properties via fluorescent imaging with biocompatibility.