An important but challenging task in single-atom catalysis is synthesizing a catalyst with controllable single-atom loading densities and no metal agglomeration. Here, we construct MoS2/rGO supports by a simple hydrothermal method and precisely control single-atom platinum (PtSA) loading density by its targeted growth on MoS2 for electrocatalysis. Using the optimized geometric and electronic structure, PtSA-MoS2/rGO exhibits an ultra-low overpotential of 11 mV at − 10 mA cm−2 in 0.5 M H2SO4 for electrocatalytic hydrogen evolution reaction (HER). First-principles calculations reveal that enhanced density of PtSA on the MoS2 surface favors the reduction of Gibbs free energy of hydrogen adsorption, facilitating the kinetic process of electrocatalytic HER. This work provides a new engineering route to fabricating a series of performance-tunable single-atom catalysts with controllable locations and loading densities.