Abstract Microcoleus vaginatus has been regarded as the important contributor for biocrust formation and ecological services. However, little is known about its living forms in biocrusts, and whether the living form is related to biocrust structure. Therefore, in this study, natural biocrusts collected from the Gurbantunggut Desert were divided into different aggregate/grain fractions, aiming at investigating the living forms of M. vaginatus in biocrusts at fine scale, and exploring its roles in aggregate structure and ecological functions of biocrusts. The results showed that two distinct living forms of M. vaginatus had been identified from the biocrusts. The non-bundling M. vaginatus was mainly distributed in the fractions of > 0.5 mm, forming aggregate structure by cementing sand particles firmly; while the bundling M. vaginatus, distributed mainly among the free sand particles with diameter < 0.5 mm, and easily migrated up to biocrust surface after hydration. Furthermore, the aggregate structure formed by non-bundling M. vaginatus supported a higher biomass, nutrient contents, and enzyme activities. Altogether, our results suggest that the strong migrating ability of bundling M. vaginatus contributes to the environmental adaptation and light resource acquirement, while non-bundling M. vaginatus acts as the constructor of the aggregate structure in biocrusts.