Stable carbon isotopes (δ13C) and elemental stoichiometry characteristics are important ways to research the water and nutrient use strategies of plants. Investigating the variation patterns inof δ13C and the major nutrient elements in different organs of plants and the correlation among them can reveal the ecological strategies of desert plants in extreme arid environments. In this study, two typical desert plants, Alhagi sparsifolia and Karelinia caspia, were studied in the Tarim Basin. By analyzing the changes in δ13C, carbon (C), nitrogen (N), and phosphorus (P) and the ecological stoichiometry of their roots, stems, and leaves, the distribution patterns among different organs and their correlation with soil environmental factors were revealed. The results showed the following: (1) The δ13C of the two plants differed significantly among different organs (p < 0.01). The root and stem of Alhagi sparsifolia had significantly greater δ13C than the leave, while the δ13C of Karelinia caspia showed a root > stem > leaf gradient; (2) the C content in the leaves of the two plants was significantly lower than that of the root (p < 0.01), whereas the N content showed the opposite trend (p < 0.01); (3) the average N:P of Alhagi sparsifolia was >16.00, indicating it was mainly limited by P elements, while the average N:P of Karelinia caspia was <14.00, suggesting it was mainly limited by N elements; (4) in the root, stem and leave of Alhagi sparsifolia and Karelinia caspia, the N content and C:N and the P content and C:P showed a significantly negative correlation (p < 0.01), and δ13C was negatively correlated with C:P; (5) soil total phosphorus (TP) is an important soil environmental factor affecting δ13C and the nutrient elements in Alhagi sparsifolia and Karelinia caspia. This study demonstrates that Alhagi sparsifolia and Karelinia caspia are able to effectively coordinate and regulate their water, N, and P use strategies in response to environmental stress. These results can provide scientific reference for the evaluation of plant physiological and ecological adaptations for ecological conservation in arid areas.