Based on the pilot area of a sponge city in Northwest China, the MIKE FLOOD models of urban flood and nonpoint source pollution are established. The uncertainty analysis of model shows that such parameters as hydrological reduction factor, imperviousness, and decay constant have big influences on the total runoff, peak flow, and water quality. The measured data of the rainfall events 20160724 and 20160623 are used to calibrate and validate the model. The correlation coefficients (R 2 ) and Nash–Sutcliffe efficiency coefficient (Ens) are both over 0.65. The changes in urban rainwater runoff and water quality for different rainfall conditions under traditional development (TD) and low impact development (LID) modes are simulated. The results show that: (1) Compared with TD mode, for different rainfall conditions under LID mode, the reduction rates of overflow and the overload pipes are, respectively, 22.4–100 and 0–54.55% when the area proportion of LID measures is 17.76%. The total runoff reduction rate is 64.01–81.52%, the peak flow reduction rate is 0–69.09%, and the flood peak time is delayed by 0–48 min. (2) Compared with TD mode, after adding LID measures, the load reduction rates of total suspended solids (SS), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) are increased by 19.20–68.71, 19.19–67.78, 18.72–60.91, and 19.89–68.75%, respectively. The effluent reduction rates of the event mean concentrations (EMCs) of SS, COD, TN, and TP are increased by 0.65–42.07, 0.65–40.34, 0.06–27.62, and 1.51–42.14%, respectively. (3) The LID measures have certain control on waterlogging situation, and the submerged area under different water depths and flooding durations are decreased by 11.11–100 and 32.23–100%, respectively. For 19.2 mm rainfall event, under the LID mode, the SS load reduction rate achieves 60%, and rainfall runoff is all assimilated without discharge and waterlogging phenomena. LID measures have a better control effect on water quality and water quantity of urban rainstorm runoff; however, the effect of LID measures will reduce with the increase in recurrence interval.