The essence of plant ecological stoichiometry is to study the relationships between species and their environment, including nutrient absorption, utilization and cycling processes as well as the nutrient limitation of plants. Plants can regulate nutrient elements and adapt to environmental changes. To understand the adaptation mechanism, it is important to take plants as a whole and quantify the correlation between the chemometrics of different organs. Ammopiptanthus mongolicus is within the second-class group of rare–endangered plants in China and is the only evergreen broad-leaved shrub in desert areas. We analyzed the ecological stoichiometric characteristics of leaves, stems, roots, flowers and seeds of A. mongolicus in five habitats, namely fixed sandy land, semi-fixed sandy land, stony–sandy land, alluvial gravel slope and saline–alkali land. We found that (1) 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. Additionally, (2) the contents of C, N, P and 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, (3) the C:N and N:P ratios in each organ were relatively stable among different habitats, whereas the K:P ratio varied greatly. The N:P ratios of leaves were all greater than 16 in different habitats, indicating that the growth was mainly limited by P. Moreover, (4) except for the P element, the content of each element and its stoichiometric ratio were affected by the interaction between organs and habitat. Habitat had a greater impact on C content, whereas organs had a greater influence on N, P and K content and C:N, C:P, C:K and N:P.