AbstractTransition metal phosphides (TMPs) are promising hydrogen evolution reaction (HER) electrocatalysts, but the unsatisfying activity and durability at industrial‐scale current densities hinder their application. Downsizing TMPs to nanoclusters can substantially enhance their activity; yet, the high surface free energy tends to initiate agglomeration thereby limiting their service life. Herein, a molecular engineering strategy to synthesize robust sulfur‐doped RuP2 (S‐RuP2) nanoclusters, which can continuously provide ampere‐level current densities of 1.0, 2.0, and 3.0 A cm−2 for at least 480 h with low overpotentials of 55.6 ± 1.0, 90.6 ± 1.2, and 122.8 ± 1.0 mV, respectively, is proposed. In particular, it exhibits a remarkable charge transfer amount (representing a long service life), outperforming all reported alkaline HER electrocatalysts. Remoulding the RuP2 architecture by sulfur atom can significantly lift the d‐band center of Ru and the p‐band center of P, therefore strengthening the adsorption of H2O, H, and OH to reduce the barriers of water dissociation and H migration. The authors‘ research unveils the enormous potential of molecule‐based porous materials for designing high‐performance nano‐structured catalysts.