To analyze the effect of sponge measures on the reduction of rainwater runoff at the watershed scale, this study presented an optimal combination mode for the construction of sponge city system. An integrated flooding and water-logging model for the Macao River was established based on the Infoworks ICM model and following the code for the design of storm water management and harvest engineering to quantitatively evaluate the storage effect of storage ponds, hollow grassland and the permeable pavement sponge combination mode. The results show that the sponge combination measures have better effect on the reduction of rainfall runoff, flood peak discharge and flood peak time in the low-recurring period of less than 10 years. In comparison while the return period of rainfall reaches 10 years and above, the reduction ratio of runoff and flood peak discharge decrease to different extents, and the flood peak discharge reduction and flood peak time delay significantly decrease. After the implementation of the sponge measures, the annual runoff of the basin was reduced by an average of 39%, when all controlled blocks meet the control standards. Current design standards for rainwater can help support the pilot construction of sponge cities.