[Background] Desertification is a major environmental problem, biological soil crusts (BSCs) can inhibit desertification, and the diazotrophs play an important role in the formation and development of BSCs. However, the community structure and diversity of diazotrophs in BSCs are not clear enough. [Objective] To clarify the community structure and diversity of diazotrophs in different types of biological soil crusts (BSCs) and soils under them and the effectors of soil environmental factors. [Methods] Using dilution heat method and alkali solution diffusion to measure the content of organic matter (OM) and the available nitrogen (AN) of soil, respectively; nifH gene was sequenced via the high-throughput sequencing platform, and the community structure, diversity and the variance analysis of diazotrophs were analyzed by bioinformatics analysis; Canonical Correlation Analysis (CCA) were used to analyze the correlation among the community structure, samples and the physico-chemical parameters of soil. [Results] Dominant phylum were Proteobacteria and Cyanobacteria in moss crusts (HSM), Cyanobacteria in the other types of BSCs; the class of Alphaproteobacteria and Betaproteobacteria accounted for the most fraction in the soil underneath moss crusts (nifH was only detected in soil underneath moss crusts, HSMs); significant differences existed in community structure at genus level, algae crusts (HSA) was predominated by unclassified_f_Nostocaceae (90.99%), Lichen crusts (HSL) by Scytonema (45.85%) and unclassified_f_Nostocaceae (44.14%), HSM by unclassified_f_Nostocaceae (29.21%), Scytonema (22.57%), Nostoc (15.34%), Skermanella (14.74%), unclassified_o_Nostocales (10.60%), and HSMs by Skermanella (33.80%), Azohydromonas (25.66%), unclassified_p_Proteobacteria (18.20%) and unclassified_c_Alphaproteobacteria (10.62%). [Conclusion] The community structure and diversity of diazotrophs in Algae, Lichen and Moss crusts and soil underneath crusts were markedly different, and the community species and the diversity increased with the development of the BSCs. This study provides a basis for appreciation and utilization of the diazotrophs in the BSCs.