Determining the proportion of shared responsibility is the most significant issue in the practice of watershed ecological compensation. According to the stages of river pollution control and ecological restoration, a model of three stages watershed ecological compensation responsibility sharing is proposed, which involves the trial stage, the restoration stage, and the stabilization stage. In the trial stage, the goal is pollution control and water quality improvement. Cost is shared by the upstream area, the downstream area, and the central government, and the proportion afforded by the central government will decline in three years. In the restoration stage, the goal is ecological conservation and restoration, and water quality and quantity should meet the requirements at the same time. Cost is shared by the upstream area and the downstream area according to the amount of water allocation. In the stabilization stage, the goal is to achieve a win-win situation and green development of the upstream and downstream areas. The proportion of compensation responsibility is determined by the opportunity costs of the upstream area. A case study of watershed ecological compensation in Jiuzhoujiang River basin shows that, in the trial stage, the proportion of shared responsibility of the upstream Guangxi Province, the downstream Guangdong Province, and the central government in the first year is 25.00%, 25.00%, and 50.00%, in the second year is 28.50%, 28.50%, and 43.00%, and in the third year is 33.30%, 33.30%, and 33.30%. In the restoration stage, the proportion of shared responsibility of the upstream area, the downstream area, and the central government is 39.30%, 53.60%, and 7.10%. In the stabilization stage, the proportion of shared responsibility of the upstream and the downstream governments is 48.60% and 51.40%. The results can contribute to the discussion of long-term watershed ecological compensation system, and it can also be a reference for the ecological compensation responsibility sharing of the Jiuzhoujiang River basin.