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Under the native habitat conditions, the seasonal gas exchange characteristics of two natural endemic plant species, Calligonum taklimakanensis B.R. Pan & GM. Shen and Tamarix taklamakanensis M.T. Liu, which are located in the hinterland of the Taklimakan Desert, are measured and compared by Li-6400 photosynthesis system. The results indicate that temperature (degrees C), solar radiation (PAR), soil water content (SWC), and other environmental factors have obvious seasonal variations and the gas exchange characteristics of two plants have different changes in different growing seasons. For C. taklimakanensis, both in July and September, its daily changes of net photosynthetic rate tend to be obvious double peak curve, but in July its peak appeared earlier. Besides its maximum net photosynthetic rate (P-max), apparent quantum efficiency (Phi), range of effective photosynthetic radiation significantly less than that in September. Moreover, its water use efficiency (WUE) in July was also lower than that in September due to the higher transpiration rate (T-r). For T. taklamakanensis, although its daily change of net photosynthetic rate is a single peak curve in September, its peak time has not changed, and except that its WUE is higher in September like C. taklimakanensis, the maximum net photosynthetic rate (P-max), apparent quantum efficiency (Phi), light saturation point, and range of effective photosynthetic radiation has not changed or slightly declined. That is to say C. taklimakanensis select a season that habitat was better (like September) to progress relative effectively photosynthesis accumulation, in contrast, T. taklamakanensis still keep a relatively stable photosynthesis rate in different growth seasons. The difference of gas exchange characteristics of the two plants in different seasons shows that adaptation strategies of the two plants to extreme conditions in desert are different. Besides, both the higher photosynthetic accumulation rate and the higher water use efficiency in September also indicate that these two endemic desert shrubs possess the abilities and strategies to make the best of limited natural resources.