The surface charges of catalysts have intricate influences on the thermodynamics and kinetics of electrochemical reactions. Herein, we develop a grand-canonical iteration method based on density functional theory calculations to explore the effect of surface charges on reaction kinetics beyond the traditional Butler-Volmer picture. Using the hydrogen evolution reaction on S vacancies of MoS2 as an example, we show how to track the change of surface charge in a reaction and to analyze its influence on the kinetics. Protons adsorb on S vacancies in a tough and charge-insensitive water splitting manner, which explains the observed large Tafel slope. Grand-canonical calculations report an unanticipated surface charge-induced change of the desorption pathway from the Heyrovsky route to a Volmer-Tafel route. During an electrochemical reaction, a net electron inflow into the catalyst may bring two effects, i.e., stabilization of the canonical energy and destabilization of the charge-dependent grand-canonical part. On the contrary, a net outflow of electrons from the catalyst can reverse the two effects. This surface charge effect has substantial impacts on the overpotential and the Tafel slope. We suggest that the surface charge effect is universal for all electrochemical reactions and significant for those involving interfacial proton transfers.