Abstract: Two profiles, located in Wuhaizi and Nuoertu, respectively, were sampled to evaluate the annual groundwater recharge in southeast of Badain Jaran Desert using method of chloride mass balance. The mean annual recharge calculated was 0.81 mm/a and 1.24 mm/a, which account for 0.9% and 1.4% of the mean annual precipitation, respectively. This implies that the direct recharge through the unsaturated zone is negligible. Thus, the local modern precipitation infiltration recharge is not the main replenishment source of groundwater.