Ammopiptanthus mongolicus is a rare and endangered species in northwest China. It is of great significance to explore floristic composition and community characteristics to maintain the fragile ecosystem in the arid desert area of northwest China. In this paper, 26 sample sites of A. mongolicus were investigated. We used TWINSPAN to classify the communities, and canonical correspondence analysis (CCA) to analyze the relationship between species composition and ecological factors of A. mongolicus. The results showed that: (1) the species composition of A. mongolicus was mainly leguminous, gramineae, compositae and chenopodiaceae, belonging to 28 families, 63 genera and 90 species, and the floristic composition was mainly distributed in Mediterranean, north temperate zone and the world. (2) TWINSPAN classification can divide 26 A. mongolicus sample plots into 9 community types. (3) According to the ranking analysis of CCA, average annual rainfall (F = 2.8, P = 0.002), the growing season rainfall (F = 2.6, P = 0.002), available nitrogen (F = 2.1, P = 0.006), solar radiation (F = 2.1, P = 0.008), the vapor pressure (F = 1.9, P = 0.006), soil organic matter (F = 1.7, P = 0.04), latitude (F = 1.7, P = 0.006) are the main ecological factors affecting the A. mongolicus community composition, the results can provide the protection of the rare and endangered plants of Mongolia sand Holly with basic data.