Ecological compensation (EC) is essential to promote the coordinated and sustainable development of the watershed. Firstly, the synergetic development index system of the watershed EC was proposed, which includes the economic benefits, water conservation, pollution treatment, and environmental supervision. Then, the order degree of subsystems was calculated. Finally, the synergetic development level of the watershed EC was evaluated. Taking the upstream (Ma'anshan) and the downstream (Nanjing) of the Chu River as the case study area, the results showed that: (1) From 2011 to 2020, the synergetic development level between Ma'anshan and Nanjing has showed an upward trend; (2) The synergetic development level of the watershed EC in the Chu River has reached basic synergy in 2020; (3) Ma'anshan concentrates on protecting the water ecological environment while Nanjing concentrates on economic growth and water pollution control will improve the synergy degree. This study can provide references for the optimization of watershed EC mechanism, and to promote watershed coordinated development.