Rural agricultural non-point source pollution is one of the main sources of pollution load in Lake Dianchi. The interception and treatment system around the lake is of great significance to the interception of rural agricultural sewage. The previous result of our research group by comparative analysis indicated that total phosphorus (TP) concentration threshold-based control mode for the interception wells of the system is most effective. In order to achieve automated control of the system and support the efficient operation of the intelligent control platform, corresponding to the TP concentration threshold control mode, the optimized (runoff) retention rate, the influences of the recurrence interval and peak intensity position coefficient on it under the current conditions were studied. In low, normal, and high flow years, the lake entry coefficients of the rural agricultural non-point source pollution loads were calculated after interception. The results showed that: (1) when the main canal overflowed, it could minimize the pollutant load overflowed into Lake Dianchi with the existing optimized TP concentration threshold, and the corresponding ratio of the intercepted runoff to the total runoff was the optimized retention rate; (2) with the increase of the recurrence interval, the TP concentration threshold presented a decreasing trend, as well as the average concentration of pollutants intercepted and the optimized retention rate; (3) with the increase of the peak intensity position coefficient, the TP concentration threshold increased and the optimized retention rate remained steady; (4) considering interception of the system with TP concentration threshold control model, the lake entry coefficients of the rural agricultural non-point source pollution loads in low, normal, and high flow years were: COD 0.09, 0.14, 0.23, TN 0.10, 0.22, 0.31, and TP 0.07, 0.12, 0.19, respectively, which were significantly lower than those without interception. (5) with TP concentration threshold control mode, the influent concentration of pollutants in the water quality purification plant at the end of main canal could be increased effectively, as well as the operational stability of the treatment processes.