In order to promote the sustainable development of bay ecosystem, a regulation method of bay ecosystem based on environmental law is proposed. Taking the coastal bay area in Fujian Province as the research object, based on the analysis of the causes of ecosystem degradation, the energy loss in this area was assessed from three aspects of climate regulation, waste disposal and disturbance regulation. Through the establishment of objective index system, the index weight of integrated ecosystem management is determined, and the evaluation of Gulf ecosystem is completed, which provides reference for ecosystem management. The results show an increase in pollution from 2016 to 2020. By using the proposed comprehensive management and regulation method and taking corresponding ecological regulation measures, the pollution index in the area is controlled within 0.3, so that a stable downward trend of pollution can be maintained.