In order to understand the geochemical characteristics of Paleozoic reservoir fluids in Xuanjing region, Lower Yangtze area, drilling core samples from Y and D wells were tested and analyzed to study the fluid inclusion types and composition. Pressure correction was undertaken to determine the temperature and pressure environment for inclusion formation, and the influence of fluid characteristics of the Upper Permian and Lower Triassic reservoirs on the preservation of shale gas was investigated. According to petrographic observations, fluid inclusions are mainly brine and bitumen inclusions. Bitumen inclusions are mainly distributed in holes and fractures, and with smaller individuals. No visible fluorescence was observed, and the vitrinite reflectance is 3.39%–3.92%. This indicates that there had been oil and gas accumulation in the early stage of diagenesis in the study area, but due to the influence of magmatic hydrothermal solution, oil and gas underwent thermal metamorphism in the early stage, making liquid petroleum into solid bitumen. At present, oil and gas in the reservoir were largely formed in the late stage. During the continuous process in which shale was buried, light oil and gas were generated. Light oil and gas underwent magmatic and tectonic hydrothermal processes in some areas, resulting in high-temperature metamorphic cracking that formed dry gas. Moreover, nitrogen inclusions are found in fluid inclusions, forming metamorphic fluids caused by magmatic hydrothermal activities. The study shows that Paleozoic reservoirs in Xuanjing area are characterized by self-generation and self-storage. Furthermore, the mechanism of shale gas accumulation is not only related to the buried hydrocarbon generation process of shale itself, but is also related to later magmatic activity and tectonic hydrothermal transformation. Therefore, preservation conditions are generally key factors of shale gas accumulation in this area.