The construction of a rural ecological governance system of “three governance integration” is not only a practical need to promote the modernization of national ecological governance, but also a practical method to build beautiful villages and promote rural revitalization. In the current process of rural ecological governance and construction, there are subject identification and coordination dilemmas, system supply and integration dilemmas, cultural inheritance and development dilemmas, which restrict the construction and operation of the“three governance integration”rural ecological governance system. From the three aspects of cultivating subject identity, improving system rules, and reshaping ecological culture, this article consolidates the foundation of rural ecological autonomy, strengthens the guarantee of rural ecological rule of law, strengthens the support of rural ecological morality, and then enhances rural ecological governance capabilities and promotes ecological beauty Rural construction.