Abstract: To ensure the security of water quality in the Middle Route of S-N Water Transfer Canal,taking Jiaozuo as example,the groundwater inflow of check valve and its impact on main canal water quality were analyzed based on GMS. Main control factor of groundwater inflow through the check valve was water level difference between groundwater and main canal,which were positively correlated. With SO₄^2-、NH₃-N、NO₃-N as analysis factors,assuming that the water quality of the main canal was case Ⅱwater,using the method of worst case analysis,it was concluded that canal water changed into case Ⅲwater while the groundwater flowed into the canal. Under the premise that the concentration of threepollutants is below 221. 676 8,0. 067 9,and 9. 083 2 mg/L,respectively. Through the method of adverse deduce,the main canal water quality still remains to be case Ⅱ water even if the groundwater flows into the canal.