Carbon isotope ratio (δ 13C) and nitrogen isotope ratio (δ 15N) of leaf in shrubs and overground matter in herbage were measured on plant species occurring in different aged artificial sand-binding microhabitats, as well as in natural habitat at the south-eastern margin of the Tengger Desert, China. Both δ 13C and δ 15N of C 3 and C 4 plants varied widely (− 28.12 ≤ δ 13C (‰) ≤ − 23.77 and − 4.45 ≤ δ 15N (‰) ≤ 3.66 for C 3 species, respectively; and − 15.79 ≤ δ 13C (‰) ≤ − 12.63 and − 7.56 ≤ δ 15N (‰) ≤ 1.08 for C 4 species, respectively), representing the different photosynthetic pathway (C 3/C 4) environmental controls. The relative abundance of C 4 species increased over the development of the sand-fixing vegetation, and the significant differences among sites in δ 15N of C 4 plants were found. Among the microhabitats, the isotopic pattern of artificial sand-fixing community is a cluster compared to that of natural vegetation and transitional zones in C 4 plants; however, this pattern of C 3 plants is different significantly. The biological soil crust had significant effect on δ 13C of C 3 plants, not for δ 13C of C 4 plants and δ 15N of both C 3 and C 4 species. Our results also describe a distinct pattern of dual-isotopic signatures, which indicated that a different water-use source and soil nitrogen compartment occurred and may promote the coexistence of different life forms in extreme poor water and nutrients ecosystems. With respect to C 4 plants, the gramineous plants based on family — level exhibit obviously negative isotopic values (both δ 15N and δ 13C) than those of chenopodiaceous plants, indicating a high water-use efficiency of gramineous C 4 plants and more 15N depleted, and these differences may be a result of different functional groups of C 4 species. For C 3 plants, the chenopodiaceous species also show more 15N enrichment than those of plants from other families (e.g. composite, leguminous plants and others). Contrast to previous studies, the δ 15N values of leguminous plants were not closer to the δ 15N of atmospheric nitrogen gas, indicating that leguminous plants in research region used nitrogen mainly from other N sources such as soil, rain/dust, not mainly from biological fixed nitrogen. The correlation between δ 13C and δ 15N of C 3 plants (except leguminous plants) were negative significantly ( P = 0.001), while there were positive relationship between δ 13C and δ 15N in C 3 leguminous plants ( P = 0.003) and C 4 plants ( P < 0.0001), indicating that in the water and nutrient limiting region the carbon and nitrogen discriminations are dependent and linked intimately, and vary with the plant species and photosynthetic pathway.