The stoichiometry of carbon, nitrogen, and phosphorus (C:N:P) among leaves, stems, and roots reflects trade-offs in plants for acquiring resources and their growth strategy. The widely distributed plant Alhagi sparsifolia is an ideal species to study the ecological stoichiometry in different organs in response to the availability of nutrients and water in the desert ecosystem. However, which response of organs is most sensitive to environmental conditions is still unclear. To answer this question, we collected samples of plants and soils including not only aboveground leaves and stems, but also underground roots and soils from a wide range of arid areas during the growing season. The C, N, P, C:N, C:P, and N:P ratios in leaves, thorns, stems, and roots were derived to explore their relationship as well as their response mechanisms to nutrients and water spanning 1 m deep in the soil. The results showed that the order of N concentration was leaves > thorns > stems > roots, that the concentration of P in the leaves, thorns, and stems was similar, and that their values were higher than those in the roots. First, the C:N ratios in the leaves and stems were significantly positively correlated with the ratio in roots. The C:N ratios in each organ showed a significant relationship with the soil alkali hydrolyzable nitrogen (SAN) above a depth of 60 cm. In addition to SAN, soil available phosphorus (SAP) and soil organic carbon (SOC) affect the C:N ratio in the roots. Second, the C:P and N:P ratios in aboveground organs showed no correlations with the ratios in roots. The C:P and N:P ratios in the leaves and thorns have no relationship with soil nutrients, while the C:P ratio in roots was influenced by SAN and SOC in all soil layers. Finally, the N:P ratios in roots were also affected by nutrients in different soil depths at 0–20 and 60–80 cm. These results illustrate that the roots were more sensitive to soil nutrients than the aboveground parts. Our study of ecological stoichiometry also suggests a novel systematic approach for analyzing the sensitivity of responses of an organ to environmental conditions.