The ecological governance system has made significant progress in information technology construction, and digitization has become an important driving force in the construction of this system. This article delves into the digital construction path of ecosystem governance and elaborates on the practical application effectiveness of digitalization in the ecological governance system through two specific cases: intelligent water management and air pollution warning digital models. Furthermore, we adopt the TOE (Technology–Organization–Environment) model to integrate a collaborative theory with the concept of multi-center governance and innovatively propose a new model for nearshore ecological environment protection management. On this basis, we constructed an evaluation index system and established a theoretical model of the impact of environmental regulations on nearshore ecological efficiency. After empirical analysis, we found that the impact of environmental regulations on ecological efficiency in coastal areas presents a curvilinear characteristic. In the modern ecological governance system, organizational factors and technological factors are the two modules that have the greatest impact on system construction, accounting for 49% and 31% of the weight of the indicator system, respectively, followed by technological advantages and the urgency and feasibility of construction. Gender factors indicate that technology and organization are necessary factors that constrain institutional development.