In order to quantify the effect of temperature changes occurred by climate change on self-purification capacity of urban river in the future, both RCP4.5and RCP8.5-the two scenarios of climate change which were mentioned in CMIP5, and the WASP module were applied to simulate and predict DO, CBOD, nitrate nitrogen and ammonia nitrogen in Tongzhou section of Beiyun river. With the simulation result, the internal transformation processes of the above factors by responsiveness of each sub-modules were analyzed. It showed that: firstly, up to 2050, the concentration of nitrate nitrogen in the all year round and the concentration of ammonia nitrogen in April-December would increase gradually, but the concentration of ammonia nitrogen would decease in January-March of Tongzhou section of Beiyun river, which was caused by climate change; secondly, the effect on water quality caused by climate change was a comprehensive result of multiple processes, in other words, even if the water quality had no obvious change, the process of its formation mechanism might be large; and thirdly, up to 2050, the process of phytoplankton growth, denitrification process and mineralization of ammonia nitrogen of water self-purification would be affected heavily by climate change.