Abstract: In order to explore an effective and practical way of wastewater treatment for the management of heavy pollution rivers in Dianchi basin, a pilot scale of ecological pond1—horizontal subsurface flow constructed wetland —ecological pond2 (EP1—HSFCW—EP2) system was built to treat the river water of Xinyunliang river in Kunming city, and this hybrid system was operated under three different hydraulic retention time (HRT) of 1, 2, 3 days. The research indicated that EP1 and EP2 were better than HSFCW for their higher stability and stronger ability in the nitrogen treatment of river water. Among them, EP1 had the best nitrogen treatment effect in high load, played a comprehensive role of flood storage pool and sedimentation tank; EP2 was more stable in the nitrogen treatment and had a better treatment effect and landscape benefit, and could ensure the quality of final effluent water, achieved the double efficacy of EP and landscape pool. It should be considered to increase the size of HSFCW proportions due to the poorer nitrogen treatment effect of HSFCW in high load; When hybrid system operated under HRT of 3 days, 2 days and 1day, the removal rate of total nitrogen were 39.39%, 25.26% and 19.26%, and the removal rate of NH3-N were 51.98%, 29.14% and 21.18%, respectively, and all the total nitrogen removal were achieved the first class discharge standard of urban sewage treatment factory. All the NH3-N removal achieved the second class discharge standard of urban sewage treatment factory. It was suggested that 1 day should be taken as the optimal HRT parameter to this hybrid system. EP1—HSFCW—EP2 system is very efficacious in treating nitrogen of urban river, and can be one of the effective technologies for treating the heavy pollution rivers in Dianchi basin.