Strong tectonic movement brings great risk to exploration of shale gas in southern China, especially in Lower Cambrian shale with complex tectonic backgrounds, which has good hydrocarbon-generation matter but low or no gas content. In this paper, the Lower Cambrian shale from the southeast Chongqing region, located in the Upper Yangtze Platform, and the Xiuwu Basin, located in the Lower Yangtze Platform, were selected as the research objects. First, the gas components in shale gas samples were measured, then analysis of nitrogen isotopic was used to reveal the nitrogen sources. Using regional geological backgrounds, core description, and seismic interpretation, combined with the perpendicular and parallel permeability test and focused ion beam–helium ion microscopy (FIB–HIM) observation, the reasons for high content of nitrogen in the Lower Cambrian shale from the Xiuwu Basin and the Southeast Chongqing region were clarified. The results indicate that the main sources of nitrogen in the Lower Cambrian shale gas at the Southeast Chongqing region is the thermal evolution of organic matter and atmosphere. Nitrogen in the atmosphere is filled into the shale reservoir through migration channels formed by detachment layers at the bottom of the Lower Cambrian, shale stratification planes, and widespread thrust faults. Nitrogen was also produced during the thermal evolution of organic matter. Both are responsible for the low content of hydrocarbon and high content of nitrogen of shale gas in the Southeast Chongqing region. Further, the main sources of nitrogen in the Lower Cambrian shale gas at the Xiuwu Basin is the upper mantle, superdeep crust, and atmosphere. Nitrogen in the atmosphere is also filled into the shale reservoir through migration channels formed by detachment layers at the bottom of the Lower Cambrian, shale stratification planes, and widespread thrust faults. Nitrogen was also produced by volcanism during the Jurassic. Both are the causes of the low content of hydrocarbon and high content of nitrogen in shale gas in the Xiuwu Basin. Finally, destruction models for shale gas reservoirs with complex tectonic backgrounds were summarized. This research aimed to provide a theoretical guidance for shale gas exploration and development in areas with complex tectonic backgrounds.