As raindrops fall from the cloud base to the ground, evaporation below those clouds affects the rain’s isotope ratio, reduces precipitation in arid areas and impacts the local climate. Therefore, in arid areas with scarce water resources and fragile ecological environments, the below-cloud evaporation is an issue of great concern. Based on 406 event-based precipitation samples collected from 9 stations in the Shiyang river basin (SRB) in the northwest arid area, GMWL and LMWL are compared and the Stewart model is used to study the effect of spatial and temporal variation of below-cloud evaporation on isotope values in different geomorphic units at the SRB. Furthermore, factors influencing below-cloud evaporation are analyzed. The results show that (1) the change of d-excess (Δd) in precipitation at the SRB and the residual ratio of raindrop evaporation (f) vary in time and space. With regards to temporal variation, the intensity of below-cloud evaporation is described by: summer < autumn < winter < spring. Regarding spatial variation, the below-cloud evaporation in mountain areas is weaker than in oases and deserts. The intensity of below-cloud evaporation in mountain areas increases with decreasing altitude, and the below-cloud evaporation in oasis and desert areas is affected by local climatic conditions. (2) Below-cloud evaporation is also affected by local transpiration evaporation, especially around reservoirs. Reservoirs increase the relative humidity of the air nearby, weakening below-cloud evaporation. This study deepens our understanding of the water cycle process in arid areas.