Ammopiptanthus mongolicus is a rare and endangered plant in China and is the only evergreen broad-leaved shrub in desert areas. To understand the growth mechanism and survival strategy of A. mongolicus and the effects of habitats and organs on its ecological stoichiometric characteristics, we analyzed the ecological stoichiometric characteristics of leaves, stems, roots, flowers, and seeds of A. mongolicus in five habitats, namely the fixed sand, semi-fixed sand, stony sand, alluvial gravel slope land, and saline-alkali flat land. The results showed that the C content was in the order of leaf > stem > root > seed > flower, while the nutrient contents of N, P, and K were in the order of seed > flower > leaf > root > stem. The enrichment of the N, P, and K in the reproductive organs promoted the transition from vegetative growth to reproductive growth, indicating the resource allocation pattern and plant growth strategy. Additionally, the contents of C, N, P, K and their stoichiometric ratios in different organs varied among different habitat types. The storage capacity of C, N, and P was higher in sandy soil (fixed and semi-fixed sandy land), whereas the content of K was higher in gravelly soil (stony-sandy land and alluvial gravel slope), and the C:N, C:P, and N:P were significantly higher in gravelly soil than those in sandy soil. A. mongolicus had higher nutrient use efficiency in stony-sandy land and alluvial gravel slope. Furthermore, the correlation analysis of element content in different organs showed that the nutrient synergy between different organs was much higher than that in the same organ. The stoichiometric ratios of C:N, C:P, and C:K followed the order of stem > root > leaf > flower > seed, N:P followed the order of root > leaf > stem > flower > seed, N:K followed the order of stem > root > leaf > seed > flower, and K:P followed the order of leaf > root > seed > stem > flower. The C:N and N:P ratios in each organ were relatively stable among different habitats, whereas the K:P ratio varied greatly. There was a significantly negative correlation between N:P and P content (P<0.05), and the correlation with N content was not significant (P>0.05), indicating that the change of N:P ratio in A. mongolicus was mainly determined by the change of P content. The N:P ratios of leaves were all greater than 16 in different habitats, indicating that the growth was mainly limited by P. Moreover, both organs and habitats had impacts on the stoichiometric characteristics of A. mongolicus, with habitat having a greater impact on C content and organs having a greater influence on N, P, K content and C:N, C:P, C:K and N:P. Except for P element, the content of each element and its stoichiometric ratio were affected by the interaction between organs and habitat. Our study provides a theoretical basis for the protection and development of species resources of A. mongolicus, and helps to understand the overall resource trade-off and covariation strategy of plant root-stem-leaf-flower-seed.