The identification and clarification of active sites of MoS₂ have long been the focus of research efforts in hydrogen evolution reaction (HER). In this study, we constructed phase transition-induced 1T-2H MoS₂ heterojunction via lithium intercalation and evaluated the HER activity using on-chip electrocatalytic microdevices (OCEMs). The heterojunction achieved an overpotential of only 226 mV at a cathodic current density of 10 mA/cm², outperforming the basal planes of 1T and 2H MoS₂. Furthermore, density functional theory (DFT) calculations demonstrated that the charge redistribution occurs at the 1T-2H MoS₂ interface with electrons transferring from 1T to 2H MoS₂, and the interfacial S atom at the top site of 1T MoS₂ presents the smallest overpotential of 0.37 V. Moreover, the interference from highly active edge sites was avoided by precisely exposing specific active areas, quantitatively revealing the catalytic activity order of different types of in-plane MoS₂ active sites. This work enables a systematic investigation of the HER activity of various active sites in MoS₂, laying the foundation for quantitative analysis of activity in other low-dimensional materials.