Based on Shenzhen basin data, SWAT model was constructed to explore and analyze the change trend of Shenzhen surface water resources from 2009 to 2022. Based on the climate scenario in CMIP6, climate change scenario data was constructed to drive the model to study the impact of climate change on the distribution trend of water resources. The results show that: (1) The applicability of the model is well evaluated. The average annual surface water resource in the region is 21.92×108 m3, the soil water recharge is greatly affected by rainfall, the soil groundwater recharge has a significant impact on groundwater balance, the proportion of deep aquifer leakage increases significantly, the proportion of base discharge decreases, and the change of groundwater reserves increases from negative to equilibrium. (2) Soil water storage is significantly affected by the medium and high radiation scenario, and the growth rate of surface runoff and river runoff slows down under the high radiative forcing scenario.