The environmental protection of Yangtze River Delta is facing a complicated and grim situation，atmospheric compound pollution and water pollution have become common problems faced by the region. Thus，the regional environmental co-governance became an important part of environmental protection of Yangtze River Delta in recent years. In order to evaluate the levels and trends of the environmental co-governance in Yangtze River Delta，an ordering degree of regional environmental protection subsystem model and a synergistic degree of complex system model are constructed. The evaluation results showed that：the environmental protection of Yangtze River Delta is constantly towards the direction of development in an orderly，and the ordering degree of Shanghai improved significantly. In study period，environmental protection of Yangtze River Delta regions showed a co-evolution state，but the synergy degree is small，the level of the environmental co-governance in Yangtze River Delta is still relatively low. However，the coordinated development of environmental protection in Yangtze River Delta still face many constraints，such as administrative barriers，regional differences in economic development and imbalance of social participating environment protection. Therefore，promotion of the level of the environmental co-governance in Yangtze River Delta depends on the following points：Firstly，enhancing the top-level design of regional environmental cooperation，considering the differences of regional development in environmental objectives setting，making use of the experience of selected units to promote work in the entire area，and then sharing of environmental protection information through a unified regional environmental monitoring network.