Southeast Chongqing has become an important position for the growth of shale gas reserves and production in China, but the development of faults and the difference of fault sealing in this area restrict the exploration and development of shale gas. In order to evaluate the fault sealing of shale strata and its controlling effect on shale gas enrichment and high production, based on seismic, drilling, logging, experimental analysis and gas test data, the characteristics of fault development were analyzed through fault anatomy and sealing evaluation of different grades and properties, and the differential influence of faults on shale gas preservation was summarized. The fault-controlled shale gas reservoir models related to faults were established. The results show as follows. There are 3 groups and 3 grades of faults in the southeast Chongqing, which are NE-trending, near SN-trending and NNW trending. The NE-trending thrust faults are the most developed, followed by the near SN-trending strike-slip faults. Under the control of the normal stress of the fault plane, the connection between the hanging wall and footwall of the fault, and mudstone smearing, the fault sealing characteristics are different. Compressional grade III faults are generally well sealed. The sealing characteristics of strike-slip grade III faults are very different, and the lack of sealing ability of faults can easily lead to the transformation of high pressure into normal pressure. The low-grade faults of grade Ⅳ and Ⅴ are well sealed, and the natural fractures associated with the faults are developed, which improves reservoir physical properties and conductive to the accumulation of shale gas. Three fault-controlled shale gas reservoirs, such as fault-anticlinal type, reverse-reverse fault occlusion type and fault-concave type, are developed in southeast Chongqing, and the enrichment of shale gas decreases gradually. The law of enrichment and high yield and the main controlling factors of shale gas in different models are defined. It is concluded that the research results deepen the understanding of shale gas preservation conditions and enrichment laws in complex structural areas, and can provide basis and reference for high-quality shale gas exploration.