In order to provide reference for the protection of local species diversity and cultivation of economic crops as well as provide a basis for the ecosystem service function assessment of Juniperus, we investigated the coverage, abundance, frequency, etc and analyzed the responses of species composition, α diversity and β diversity to elevation gradient in the communities of Juniperus przewalskii natural forest in Maxiu forest centre and Zhongtie forest centre in Three River Headwater based on the field investigation. The results indicated that: (1) a total of 72 species were investigated in the sample plot, belonging to 27 families and 58 genera. Among them, 1 species of gymnosperms belong to 1 family and 1 genus, 61 species of dicotyledonous belong to 21 families and 48 genera, 10 species of monocotyledonous belong to 5 families and 9 genera. For Juniperus przewalskii forest, Compositae are dominant. (2) The species richness of vegetation layer was as follows: herb layer > shrub layer > arbor layer. The arbor layer was dominated by J. przewalskii, while the species richness of shrub and herb layer showed an obvious “lateral pattern” on the elevation gradient, both reaching the maximum value at 3 150 m. (3) With the rise of altitude, shrub layer and herb layer α diversity showed a “wave” shaped change trend, reaching the lowest value at 3 550 m. (4) The Cody index of shrub layer reached its peak at 2 950-3 150 m, and that of herb layer reached its peak at 3 150-3 350 m. The Sorenson index of shrub layer peaks at 2 950-3 150 m and 3 350-3 550 m, while herb layer peaks at 2 950-3 150 m. Therefore, in the process of ecological restoration, the degree of human disturbance should be controlled at low altitudes and the cultivation and utilization of local economic plants should be increased for enhancing the income of farmers and herders.