Abstract: In order to explore the institutional advantages of ecological compensation and the target assessment of river chief system in water pollution prevention and management, this paper took the Shunqing section of Nanchong City as an example to study and analyze the characteristics of water quality changes in small watershed. From 2011 to 2023, water quality changed from category V to category Ⅲ, and remained stable after 2019, the water quality was good for five consecutive years, reaching the target assessment; monthly average concentration and average concentration of five main indicators, including chemical oxygen demand, permanganate index, ammonia nitrogen, total phosphorus, and biochemical oxygen demand, their average fluctuation from March to July, and other monthly average remained stable; chemical oxygen demand and total phosphorus; dissolved oxygen showed negative correlation between dissolved oxygen and other 5 indicators. By comparing the concentration of the main indicators, the average annual concentration of the five main indicators was decreased by 42.4%～60.9%, and the increase of dissolved oxygen was up 39.8%. After 2016, the water quality of the Shunqing section has improved significantly, which showed obvious effects of water pollution prevention and control.