The Yangtze River Economic Belt, as a globally important economic growth pole and population concentration area, has always received attention to its ecological and environmental issues. Currently, there is little research on the synergy among the ecological environment risk prevention and control mechanisms in this region. Strengthening research in this area has important scientific value for improving the effectiveness of ecological risk prevention and control and the sustainable development of the Yangtze River Economic Belt. Based on the data from 11 provinces and cities in the Yangtze River Economic Belt from 2017 to 2021, this study establishes an indicator system with benefit incentive mechanisms, risk regulatory mechanisms, and risk governance mechanisms as frameworks. By employing a composite system synergy model, this study utilizes the entropy weight method to assign weights to each indicator and calculates the orderliness and synergy of the three mechanisms separately. The results show that: (1) There are differences in the orderliness of mechanisms among the regions. The downstream area has the highest orderliness of the three mechanisms, with the middle stream area higher than the upstream area in terms of incentive mechanisms and risk governance mechanisms. (2) The orderliness of each mechanism has slight fluctuations but shows an overall upward trend, with the orderliness of regulatory mechanisms significantly higher than that of incentive mechanisms and governance mechanisms. (3) In terms of synergy, the three major mechanisms show a stable upward trend in synergy but with a relatively low degree of synergy. Based on these findings, future efforts should focus on optimizing mechanism construction and information sharing, improving incentive mechanisms, strengthening risk regulatory mechanisms, and consolidating the effectiveness of risk governance mechanisms.