In the fragmented habitats, the biological characteristics of plant populations directly reflect the plant's response and adaptation to the environment. Researches on the size, density, seed setting rate, seed size, seed quality, and seed germination characteristics of plants in different fragmented habitats have important guiding significance for in-depth understanding of plants' survival and reproduction strategies. In this study, the morphological characteristics and reproductive parameters of Alhagi sparsifolia populations in nine patches at the southern margin of the Gurbantunggut Desert were investigated in 2018 and 2019. The results showed that with the increase of the degree of habitat fragmentation, the height, crown width, density, seed setting rate, seed size, seed quality, and seed germination rate of A. sparsifolia decreased significantly. The habitat fragmentation not only significantly inhibited the vegetative growth of A. sparsifolia, but also led to the sparsely distribution that seriously hindered its reproduction and population regeneration, increasing the risks of population depression and extinction.