A pot experiment with natural water consumption after artificial watering was conducted to study the effects of drought stress on water, photosynthesis, chlorophyll fluorescence in leaves of three desert species, Haloxylon ammodendron, Nitraria tangutorum and Artemisia desertorum. The change characteristics and response mechanism of each index in the process of drought stress and its quantitative relationship with soil water were discussed, and their drought resistance was ranked by membership function method. The results showed that: (1) the relative water content (RWC) of three species leaves decreased continuously with the extension of drought stress time, and the water deficit (RWD) showed a fluctuating upward trend. (2) The contents of Chl, Chla, Chlb of the three species and carotenoids in H. ammodendron and N. tangutorum was decreased with the increase of stress days. The carotenoids of Artemisia desertorum increased with the decrease of soil moisture. (3) The P_n, T_r, WUE and other main gas exchange parameters of the three species showed significant threshold response to soil water content. The suitable soil water content thresholds for normal photosynthetic physiological activities were 8.04%-19.33%, 4.17%-19.10% and 6.48%-17.51%, respectively. (4) The F_v/F_m, F_v′/F_m′ and qP of the three species decreased with the increase of drought stress days and light intensity, and NPQ showed a gradual upward trend. F_v/F_m and F_v′/F_m′ of H. ammodendron, A. desertorum decreased, photosynthetic activity was destroyed, and electron transfer was blocked. PSⅡ reaction center was damaged and showed photoinhibition after 30 days and 18-30 days of stress. However, N. tangutorum has stronger ability to regulate its PSⅡ reaction center to avoid injury. (5) The comprehensive analysis of membership function method showed that the drought tolerance of three species was N. tangutorum, H. ammodendron and A. desertorum. The results showed that all the three desert species showed strong tolerance to drought stress by adjusting the opening degree and activity of PSⅡ reaction center. At the late stage of stress, the plants PSⅡ reaction center closed or irreversibly inactivated and showed photoinhibition.