As a promising alternative to Pt/C catalyst, MoS₂ has attracted ever-growing attention regarding to its high crustal abundance, high stability, and abundant active sites at the edges, which broadens the choice scope for high-performance hydrogen evolution reaction (HER) catalyst. However, sluggish electrochemical kinetics from the inert base plane of MoS₂ greatly hampers its practical application. Fortunately, the local chemical and atomic structure of MoS₂ can be rationally tuned by doping strategies, offering great opportunities to activate the basal plane. In this review, advances on metal-doped, nonmetal-doped, as well as vacancy-doped MoS₂ and their atomic-level structure are comprehensively summarized, and a deep understanding of the structure–activity relationship for HER catalyst design is provided. Furthermore, current challenges in this field and future prospect initiated by the development of advanced characterization methods are presented.