The southern margin of the Sichuan Basin is characterized by strong structural deformation, complex fault structure styles and scales, and multistaged geological evolution stages, which together have created various shale gas preservation conditions. Taking Jianwu (JW)–Luochang (LC)–Shuanglong (SL) synclines as an example, the fault development characteristics and structural styles of the Longmaxi Formation were studied based on fine seismic interpretation and microscopic tests (rock acoustic emission experiments and fracture-filling inclusion tests), and the effects of the fault stage, fault class and scale, and fracture development degree on shale gas preservation conditions were analysed. Basement-involved faults, detachment faults, and intraformational microfaults are mainly developed from southeast to northwest. These fault structural types have affected the JW Syncline in the southeastern part, where faults are developed from the bottom of the Cambrian to the Wufeng–Longmaxi Formation and from the Wufeng–Longmaxi Formation to the Permian (Triassic). The SL-LC region in the northwestern part is dominated by the faults from the Wufeng–Longmaxi Formation to the Permian (Triassic). This region is dominated by NE-trending main control faults, supplemented by NW-trending, approximately EW-trending, SN-trending, and other small-scale regulating faults. Fault development can be divided into three stages, corresponding to the early, middle, and late Himalayan tectonic movements. In the early stage, a few small-scale approximately EW-trending faults had little impact on shale gas preservation. In the intermediate stage, the large number of large-scale NE-trending main control faults significantly impacted shale gas preservation. The JW Syncline mainly developed three types of faults with a high-filling degree, weak upwards penetration, and small-scale relevant fractures, which together created favourable conditions for shale gas preservation. The western and northern parts are dominated by I and II faults with large structural deformation, a low-filling degree, a large-scale, and strong penetration of related fractures, which have created unfavourable conditions for shale gas preservation. During the late stage, approximately SN- and NW-trending strike-slip reverse faults developed, and strong shear and fracture zones formed near the faults, producing unfavourable conditions for shale gas preservation. This research has clarified the characterization method of fault characteristics and stages and has established the influence of complex faults on shale gas preservation, which has an important reference value for the exploration and evaluation of shale gas reserves in complex tectonic regions.