Abstract: Objective The objective of this study is to elucidate the genesis mechanism of the geothermal system in the Yangyuan Basin, Zhangjiakou. This addresses a key scientific gap, as its genetic model has not been systematically explained, a deficiency that restricts the selection of high-quality exploration targets. Methods This study employed an integrated analysis of geological, geophysical, hydrogeochemical, and isotopic data. Furthermore, a comparative study with the neighboring Datong Basin was conducted to highlight the unique characteristics of the Yangyuan system.Results The results of this investigation show that geophysics reveals a deep thermal anomaly beneath the basin, associated with Datong volcanic activity. The reservoir system exhibits a dual-layer structure, dominated by Jixian carbonates, with localized Archean metamorphic fractures. This reservoir is overlain by thick Cenozoic sediments that act as a competent caprock. NW-trending deep faults and NE-trending basin-controlling faults provide pathways for fluid circulation and migration. The geothermal fluids originate from meteoric precipitation and undergo deep circulation and heating. Three genetic models were identified within the basin: fault-zone convective, deep-depression conductive, and fault-uplift composite. Conclusions The findings of this study indicate that the Yangyuan geothermal system concurrently possesses the high-quality reservoirs typical of stable cratonic basins and the active heat sources and pathways characteristic of rift zones. This reflects the composite nature of a tectonic–thermal transition zone. The polygenetic models proposed in this research provide a new theoretical framework for geothermal resource exploration within the rift basins of North China.