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In Gurbantunggut Desert, cyanobacterial and microalgal components were characterized within 60 soil samples collected from sand dunes. Fifty-one taxa of cyanobacteria and algae were identified. Without exception, the soils were alkaline, poor in nutrients, and showed large variations in other soil properties. Spatial heterogeneity for distribution of cyanobacteria and microalgae (diversity of morphotypes, species composition, and microbiomass) existed. Compared with other deserts in the world, the Gurbantunggut Desert has a greater diversity of cyanobacterial-microalgal morphotypes. Results from step regression showed that the diversity of morphotype was determined by total P, available P, and soil layer. Filamentous cyanobacteria dominated the community. Microcoleus vaginatus (Vauch.) Gom was the dominant species in most positions on sand dune, while the abundance of other dominant species varied depending on the sand dune position and the soil layer in which they occurred. The microalgal biomass was influenced by the content of Mg, crust type, soil moisture, sunlight, and oxygen concentration. A significant positive relation was found between microalgal biomass and diversity of morphotype. Species composition, diversity of morphotype, and microalgal biomass interacted with each other. The contents of P and Mg ion, soil texture, and soil moisture may be the main factors responsible for cyanobacterial-microalgal distribution.