In order to accurately estimate the groundwater recharge due to irrigation deep percolation, the groundwater recharge coefficients were calculated based on changes of groundwater level and soil water content before and after water application jointly using field experiment method and numerical simulation method, and the results were verified using numerical simulation based on principles of soil water dynamics. The groundwater recharge coefficients were 0.15 and 0.3 for crop growth period and autumn respectively. With a shallow groundwater level in Hetao irrigation district, the results from change of groundwater and numerical simulation showed that the groundwater recharge reached maximum at 2-4 days after water application and groundwater recharge process completed at 8-10 days after water application. The deep percolations of different water applications followed the same pattern and the groundwater recharge and time were closely related to water application. The research results may provide a reference to the determination of threshold value of water diversion for sound development of ecological environment of the district.