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Gymnocarpos przewalskii is a rare Tertiary relict species, mainly distributed in desert areas of northwestern China. Changes in rainfall have a significant impact on the physiological characteristics of desert plants. In the present study, the effects of five simulated rainfall levels on the gas exchange parameters, chlorophyll fluorescence characteristics, and antioxidant system of G. przewalskii were studied. The results show that with increased rainfall the net photosynthetic rate (Pn) and transpiration rate increase significantly. The reduction in Pn is caused by stomatal and non-stomatal limitations under decreased rainfall. Decreased rainfall markedly improves the instantaneous water-use efficiency of leaves. With increased rainfall, the maximum photosynthetic rate, apparent quantum efficiency, and light utilization range significantly increase. Under reduced rainfall, the chlorophyll content, maximum photochemical efficiency of PSII, and steady-state optical quantum efficiency decrease and photoinhibition is caused in the PSII system. A rainfall reduction of 30% leads to massive production of superoxide anions and hydrogen peroxide, causing obvious peroxidation damage. Meanwhile, superoxide dismutase, peroxidase, and catalase in the leaves are significantly enhanced to remove excess reactive oxygen species and alleviate the injury to photosynthetic apparatus. Our study reveals the effect of rainfall changes on the photosynthetic characteristics and antioxidant system of G. przewalskii, and can improve understanding of the adaptive strategies of desert plants under future precipitation changes in northwestern China.