The genesis of unconformities involves multiple influences on basin formation and evolution, which affects the favorable reservoir and hydrocarbon distribution. Within the Early Triassic Baikouquan Formation in the Mahu Sag of the Junggar Basin, we identified subaerial unconformities (SU), namely SU1 and SU2. SU1 is characterized by regional, irregular valleys, whereas SU2 displays extensive lateral extent with comparatively lower relief. These distinctions stem from detailed analyses involving cores, well data, seismic profiles, and spatial distributions, enriching our understanding of SUs in the Junggar Basin. Key findings from our study include: (1) SU occurrences within the Baikouquan Formation span the falling-stage systems tract (FSST) and expanding system tract (EST), corresponding to relative lake level changes. SU1 emerges during descending lake levels, whereas SU2 develops during rising levels. (2) The extensive uplift of the Junggar Basin's perimeter, driven by the late Hercynian movement, heightened topographic gradient shapes a steeper lake shoreline profile, fostering SU development. Arid paleoclimatic conditions during the Permian-Triassic interval accelerate SU formation in the FSST. (3) SU typically comprises regional compound scour surfaces (RCS) and river intermittent exposure surfaces (IES). Continuous winnowing at RCS led to relatively high primary porosities, IES can develop better secondary porosity with superposed freshwater leaching. The investigation into the subaerial unconformity in the study area holds broader implications for comprehending depositional processes, reservoir distribution, and petroleum prospects, both locally and within a global lake basin context.