The in situ characterization of the heterostructure active sites during the hydrogen evolution reaction (HER) process and the direct elucidation of the corresponding catalytic structure-activity relationships are essential for understanding the catalytic mechanism and designing catalysts with optimized activity. Hence, exploring the underlying reasons behind the exceptional catalytic performance necessitates a detailed analysis. Herein, we employed scanning electrochemical microscopy (SECM) to in situ image the topography and local electrocatalytic activity of 1T/2H MoS2 heterostructures on mixed-phase molybdenum disulfide (MoS2) with 20 nm spatial resolution. Our measurements provide direct data about HER activity, enabling us to differentiate the superior catalytic performance of 1T/2H MoS2 heterostructures compared to other active sites on the MoS2 surface. Combining this spatially resolved electrochemical information with density functional theory calculations and numerical simulations enables us to reveal the existence of hydrogen spillover from the 1T MoS2 surface to 1T/2H MoS2 heterostructures. Furthermore, it has been verified that hydrogen spillover can significantly enhance the electrocatalytic activity of the heterostructures, in addition to its strong electronic interaction. This study not only contributes to the future investigation of electrochemical processes at nanoscale active sites on structurally complex electrocatalysts but also provides new design strategies for improving the catalytic activity of 2D electrocatalysts.