Technological innovation can promote high-quality economic growth. This paper discusses the promotion of green total factor productivity from the perspective of collaborative innovation in the Yangtze River Economic Belt. Firstly, the evaluation index system of collaborative innovation level is constructed from two aspects of collaborative innovation elements and collaborative innovation environment. Then the entropy method is used to measure its development level. The results show that the collaborative innovation level of provinces in the Yangtze River Economic Belt presents an increasing trend year by year. Meanwhile, there are regional differences, which is characterized by 'high in the middle reaches, middle in the downstream and low in the upstream' Secondly, the SDM model based on endogenous spatio-temporal weight matrix is constructed to analyze the influencing factors of green total factor productivity. The results show that collaborative innovation in the Yangtze River Economic Belt has significant negative impact on green total factor productivity in terms of spatial interaction and fiscal expenditure also has a negative impact. The spatial interaction between environmental protection and opening up has a significant positive impact on green total factor productivity. However, the spatial interaction between industrial structure and human capital on green total factor productivity is not obvious. Finally, this paper puts forward some policy suggestions to improve green total factor productivity.