The distribution of endophyte in host plant tissue is an important mechanism of endophyte adaptation to the outside world. Based on the Illumina MiSeq sequencing technique, the endophytic 16SrRNA and ITS rDNA in the leaves and roots tissues of O. glacialis, which are the main locoweed plants adapted to the extreme environment of Qinghai-Tibet Plateau, were analyzed by high-throughput sequencing and bioinformatics analysis. By clarifying the structure and function of endophytes in O. glacialis tissue and the relationship between environment and them, the possible influence of the distribution characteristics of endophytes on the adaptation of O. glacialis to extreme environment was discussed. The results showed that the abundance of co-genera in O. glacialis tissues accounted for more than 90% of the total abundance, and the community structure characteristics of coexistence of conservative endophytic bacteria and specific endophytic fungi were formed among different tissues. The effects of plant tissue structure and environment may provide impetus for endophyte to choose appropriate tissue niche colonization, in which soil moisture content significantly affects the Beta diversity of endophytic bacteria (R²=0.241, P=0.024) and endophytic fungi (R²=0.223, P=0.031), and soil pH value mainly affects the Alpha diversity richness index of endophytic fungi (R²=0.571, P < 0.001). However, the explanation of significant differences in endophyte function and nutritional type among tissues by environmental factors is not significant. It is considered that the conservative and different endophytic community structure and function provide help for different plant tissues to adapt to the extreme environment, which is beneficial to the survival and diffusion of O. glacialis.