Nanyuan Tongxian fault is one of the most important hidden faults in Beijing plain area. The study of its structural characteristics and activity is an important work to optimize the spatial pattern of Beijing's territory and urban geological security. The structural characteristics and activity of the Nanyuan-Tongxian fault were discussed by means of controlled source geoacoustic sounding and high precision gravity exploration, combined with drilling and stratigraphic profiling and geochronology measurement. The results show that the Nanyuan-Tongxian fault has good ductility in the southern area of Beijing, and the fault trace is well reflected in the controlled source audio magnetotelluric sounding and gravity profile. Based on the analysis of borehole profile and borehole chronology, it is found that the fault has no strata above the Middle Pleistocene. It is considered that the South west section of Nanyuan Tongxian fault has been inactive since the Middle Pleistocene. The occurrence of Neogene magma in the borehole also proves the accuracy of fault zone location, and it is inferred that the basalt magma originates from the upwelling of the asthenosphere mantle and the extensional activities of the major faults in the region. The research findings of this paper not only fill the gap in the study of the activity of the southern section of the Nanyuan-Tongxian fault, but also provide important scientific support for urban geological safety and land development in the southern part of Beijing, which has important theoretical and practical significance.