As a Chinese endemic species, Nitraria tangutorum Bobr. distributes in Qaidam Basin undergo intensive environmental stress, especially in climate change. To investigate the distribution characteristic of simple sequence repeats (SSRs) and develop SSR marker for genetic diversity research, we developed SSRs based on transcriptome data and investigate the distribution characteristic of SSRs, and selected 23 pairs of for genetic diversity analyze. The result showed that the frequency of SSR site is 49.97%; AG/CT and AAG/CTT are the dominant repeat units. A total of 126 alleles were detected; the Ne, He, Ho and Shannon’s index are 2.581, 0.588, 0.604 and 0.987, respectively, and the Fst and Nm are 0.039 and 6.243. About 5% of the variation come from population, and 95% of the variation came from individuals. Six populations are divided into two genetic clades which are different with Geographical distance distribution. Fragmentation of habitat is the main reason for the differentiation between populations, and human interference is the main reason for reducing population diversity. Therefore, the protection of this plant should minimize unreasonable human development and utilization, focus on in-situ protection, pay attention to its habitat protection and pest control, and actively carry out the collection and genetic improvement of germplasm resources.