In order to study the rainfall-runoff relationship under the changing environment in Zhengzhou City, using the annual precipitation and runoff of Zhengzhou City from 1963 to 2012 as the basic data, the runoff catastrophe point was determined by using the time catastrophe theory as the change point of rainfall-runoff relationship, and the rainfall-runoff relationship on multiple time scales was studied by combining multi time scale wavelet analysis and set pair analysis. The results show that the annual precipitation in Zhengzhou City has no obvious change trend, the annual runoff has a significant mutation in 1985 and 2002, and the rainfall-runoff relationship is becoming more and more complex. The annual precipitation in Zhengzhou City has a fluctuation period of quasi 2—4a, 5—7a, 6—11a, 23a and 32a, while the annual runoff has a fluctuation period of quasi 2—4a, 4—9a, 8—11a and 17a. The uncertainty relationship between rainfall and runoff in Zhengzhou City is dominated by identity in short, medium and medium long periods and difference in long periods, and the three time periods divided according to variation years basically accord with this law.