Abstract: The Shishou section of the Yangtze River has long been an important habitat for the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and was designated as a national freshwater dolphin nature reserve in 1992. In recent years, efforts to protect the Yangtze River ecosystem have led to a noticeable recovery of aquatic biological resources across the Yangtze Basin. Recent survey results show a significant increase in the population of the Yangtze finless porpoise, with predictions suggesting a forthcoming period of stable growth. As a key protected area for this species, accurately understanding the ecosystem status and porpoise population dynamics in the Shishou section will provide more comprehensive and scientific management measures for the continued growth. This study constructed an Ecopath model of energy flow in the Shishou section to assess the environmental capacity for the Yangtze finless porpoise. The results indicate that the effective trophic level range from 1.000 to 3.153, with the Yangtze finless porpoise at the highest trophic level, followed by the Culter mongolicus functional group. The energy flow in the food web mainly occurs through three pathways: two grazing food chains and one detrital food chain, forming a pyramid structure but with a low total transfer efficiency of only 2.63%. Indicators of ecosystem maturity and stability suggest that the Shishou section ecosystem remains in an immature state and requires further stability improvement. According to the model’s energy flow balance principle, the environmental capacity for the Yangtze finless porpoise in the Shishou section is estimated at 0.055 t/km², equivalent to about 107 individuals. Further model simulations predict that with an increase in porpoise biomass, the overall ecosystem scale and maturity will slightly increase, while stability will remain relatively stable. Appropriate increases in plankton-feeding and herbivorous fish could significantly enhance the environmental capacity for the Yangtze finless porpoise and improve ecosystem conditions. The results of this study provide important reference for the development of protection strategies for the Yangtze finless porpoise in the Shishou section and offer baseline data for evaluating the effectiveness of the “Ten-Year Fishing Ban”.