The determination of the non-stationary design flood is an integral part of the planning and designing of water conservancy projects, as well as the decision-making of flood control. Aiming at the disadvantages of limited application of the annual non-stationary value obtained by the conventional time-varying moment method, we employed the expected number of exceedances (ENE) of return period to investigate the non-stationary design flood of the Qiujin Hydrological Station in the Xiuhe River Basin with the consideration of meteorological factors of precipitation and air temperature derived from the downscaled general circulation model (GCM). The flood series of annual maximum 1-day, annual maximum consecutive 3-day, 7-day, 15-day and annual maximum 1-month of the Qiujin Hydrological Station from 1956 to 2014 were analysed to obtain the non-stationary design flood of multiple time scales, which were then compared with those of the conventional method. Results showed that the location parameter of all the above five series suffered from significant non-stationarity; the design flood values were of great difference between the stationary models and the non-stationary models with precipitation and temperature as covariates. Particularly, at the return periods of 20 a and 50 a of each time scale, the non-stationary design values reduced by about 13.5%-32.6% (about 26.4% average) and 15.3%-39.1% (about 31.0% average) under the scenarios of RCP4.5 and RCP8.5, compared with the stationary ones. This research may provide a contribution to the regional flood disaster prevention and the reuse of flood resources.