Transition metal (TM) doping has been demonstrated to be an efficacious way to boost the catalytic activity of molybdenum disulfide (MoS2) for energy storage and conversion, especially for the hydrogen evolution reaction (HER). Real-space visualization of the atomic structure of Ni doped MoS2 is crucial to understand the role of heteroatoms in enhancing electrocatalysis. By utilizing aberration corrected scanning transmission electron microscopy (STEM), we found that Ni dopants occupy Mo sites in MoS2 synthesized by a one-pot hydrothermal method. Such selective occupation of the single-atom Ni dopants leads to significant lattice distortion and electronic structure modification of the catalytically inert basal planes of MoS2, which are responsible for the enhanced HER catalysis of MoS2 in both acidic and alkaline solutions.