By the method of geostatistics, this paper studied the spatial heterogeneity of plant community species diversity in Ejina Oasis at the lower reaches of Heihe River. In the study area, the Margalef richness index (Ma), Simpson diversity index (Ds), Shannon diversity index (H') and Pielou evenness index (J') were in normal distribution, and the coefficient of variation (CV) ranged from 55.8% to 67.8%, suggesting a moderate variability. The Ma and H' were accorded with exponential models, and the Ds and J' were accorded with spherical models. The H' had the highest extent of spatial variation, followed by Ma, J' and Ds. Within the variable range, the structural factors in the spatial variation of Ma, Ds, H', and J' were dominant, ranging from 81.1% to 93.0%. The indices changed obviously parallel to the river, with significantly high values near Dalaihubu Town (42 degrees N, 101 degrees E), and obviously low values within the strips 100 degrees-101 degrees E and 102 degrees-102 degrees 30' E, mainly including east and west Gobi and the hinterland of Badain Jaran Desert.