The Yesso scallop, Patinopecten yessoensis, is a large-scale fine marine cultured shellfish and is currently the most economically valuable cold-water species in the scallop family in the world. Since it was introduced to China in the 1980s, it has been mainly cultivated in the northern waters. Zhangzi Island is China’s largest scallop bottom sowing base, where the scale of cultivation has increased from 600,000 mu in the 1980s to 1.3 million mu in 2017. However, the rapid development of Zhangzi Island Marine Ranch has seen the large-scale death of Yesso scallops, and the bottom sowing industry is facing extremely severe challenges. We aimed to strengthen systematic research on the environmental effect of mariculture and investigate the sustainable development of bottom-seeded multiplication marine ranches. The existing methods for evaluating the ecological capacity of the Yesso scallop on Zhangzi Island include the parameter index method and the numerical model method. In this study, we used Ecopath with Ecosim 6.5 (EwE) software to construct the Ecopath model of the Zhangzi Island sea area and analyzed the trophic structure and energy flow characteristics of the Zhangzi Island sea ecosystem, as well as evaluated the ecological capacity of the bottom sowing and proliferation of Yesso scallops. The results indicated that 1) the trophic level of the Zhangzi Island marine ecosystem was between 1 and 4.365. The lowest trophic level of one was occupied by phytoplankton and organic debris. The highest trophic level was the stingray functional group with a trophic level of 4.365. The average conversion efficiency between the trophic levels of the grazing food chain was 6.268% and the average conversion efficiency between the trophic levels of the detritus food chain was 7.698%. The energy flow of the system was predominantly the detritus food chain. The total system conversion efficiency was 6.923%, and the Lindemann conversion efficiency was lower than 10%. The system connection index was 0.219, the system omnivorous index was 0.174, the system Finn cycle index was 7.790, and the average path length of the Finn system was 2.674, indicating that the energy of the system was not fully utilized and there was a case of energy transmission blocking. Comparing our results with those of previous Ecopath model data for Zhangzi Island ecosystem, it was found that these values have increased annually, indicating that the ecosystem is in a state of continuous development. 2) The ecological capacity of the Yesso scallop estimated by the model was 36.805 t/km2 , 17.5 times higher than that of the existing stock; the total primary production/total respiration of the Zhangzi Island ecosystem before and after reaching ecological capacity exhibited little (0.26) change, the system omnivorous index and the system connection index did not change significantly and, thus, did not have a significant effect on the stability and nutritional structure of the Zhangzi Island ecosystem. Therefore, there is still great potential for the growth of the Yesso scallop population on Zhangzi Island.