Abstract: To more accurately evaluate the health status of the river and identify the main obstacle factors affecting the river health, this paper adopted the four-element connection number method to scientifically calculate the connection degree between the evaluation indexes and the standard grades, determines the subsystems of the river health evaluation and the sample grade values by the level eigenvalue method, identifies the subsystems affecting the health of the river, and adopts the four-element common subtraction set pair potential and four-element semi-partial subtraction set pair potential to identify the main obstacle factors affecting the health of the river in a quantitative manner. The main obstacle factors were quantitatively identified by using four-element common subtraction set pair potential and four-element semi-partial subtraction set pair potential, and the river health evaluation analysis method based on four-element subtraction set pair potential was constructed and applied to the Shiwuli River. The study results indicated that the health grade value of Shuishili River was 3.03, falling within the range of unhealthy to diseased, suggesting an overall unfavorable health status. The results were highly consistent with existing literature data: the hierarchical values of the pressure subsystem were 2.65, the status subsystem was 3.16, and the response subsystem was 3.11. The main subsystems affecting the health status of Shuishili River were the pressure subsystem and the response subsystem. The quadratic subtractive set of pairwise potentials can quantitatively reflect the state of the evaluation indicators, and the main obstacle factors affecting the health of the river were identified such as COD discharge A3 and ammonia emission intensity A4 of the pressure subsystem. Eight indicators, such as ecological flow demand guarantee rate A7 of the state subsystem, comprehensive water quality index A8, and four indicators, such as early rainfall collection rate A17 of the response subsystem and wastewater treatment rate A18 can also reflect.