In the context of global climate change, plant functional traits changes are the hot research area in the ecology field concerning by a lot of researchers. As the most direct organ in contact with the external environment, plant leaf exhibits a greater plasticity and sensitivity, which can be represented by diverse responses in plant leaf functional traits to environmental changes. The upper reaches of Tarim River was a typical arid region, distributing many desert plants, which playing important roles in maintaining local ecological security, sandy land and saline alkali land are the most common habitats for these desert plants growing. In order to understand the functional traits of desert plant leaves and their ecological adaptability to different habitats in the upper reaches of Tarim River, two typical desert plants, Karelinia caspica and Alhagi sparsifolia, were chosen in this study. Their leaf structural and chemical traits in different habitats (including sandy land and saline alkali land) were analyzed and the relationship between these traits and soil factors were discussed combining with redundancy analysis. The results showed that:(1) there were significant differences in leaf structural traits between two studied species (P < 0.05), including leaf thickness (LT), leaf area (LA), specific leaf area (SLA), and leaf tissue density (LTD); while the differences in chemical traits were significant between two different habitats (P < 0.05), including the leaf organic carbon content (LOC), leaf nitrogen content (LN), and leaf phosphorus content (LP), their average values were 417.67 g/kg, 15.14 g/kg and 1.12 g/kg, respectively, which were lower than the average level of global plant leaves (464g/kg、18.3 g/kg、1.80 g/kg, respectively). (2) In sandy land and saline alkali land habitats, the LA of two studied plants both showed extremely significant positive correlations with SLA (P < 0.01), while the LA, SLA of two studied plants both showed significant negative correlations with LTD (P < 0.01), and LA as well as N/P were the top three common index factors of plant leaf functional traits in different habitats. (3) Redundancy analysis showed that soil factors, including soil water content (SWC), soil organic carbon (SOC), and soil nitrogen (SN) had significant effects on desert plant leaf traits. This study demonstrated that desert plants have developed relatively stable leaf structural traits in the long-term evolution, and leaf chemical traits were more sensitive to the changes in soil factors of their habitats.