The patterns of biogeographical distribution and assembly processes of microbiota are of vital importance for understanding ecological adaptation and functioning maintenance. However, the role of their morphological characteristics in microbial assembly is still poorly ascertained. Here, by integrating high-throughput sequencing and robust extrapolation of traits, we investigated taxonomic and phylogenetic turnovers of various cyanobacterial morphotypes in biocrusts to evaluate the contributions of deterministic and stochastic processes across a large scale of drylands. The results showed that the non-heterocyst filamentous category dominated biocrusts in the arid ecosystem and exhibited strong tolerance against environmental fluctuations. Despite thesignificant distance-decay relationship of β-diversity detected in all categories, both species composition and phylogenetic turnover rates of coccoid cyanobacteria were higher than non-heterocyst filamentous and heterocystous morphotypes. Moreover, the assembly of cyanobacteria was driven by different ecological processes that the entire community and non-heterocyst filamentous morphotype were governed by deterministic processes, while stochasticity prevailed in heterocystous and coccoid cyanobacteria. However, aridity can modulate the balance between determinism and stochasticity and prompt a shifting threshold among morphotypes, generating an alteration in community composition. Our findings provide a unique perspective to understanding the role of microbial morphology in community assembly, highlighting the differentiation of biogeographic distribution, environmental response, and species preference between cyanobacterial morphotypes with consideration of potential functional consequences.