【Objective】Microorganisms play an important role in the formation of biological soil crusts while biological soil crusts are important for controlling soil erosion. However, there is limited research on microbial community in the biological soil crusts of southern red soil. Therefore, the changes of microbial community structure under forest fertility improvement measures in this area are unclear.【Method】The present study was conducted in the Pinus elliotti forest of tropical Quaternary laterite in the middle subtropical zone. Organic fertilizer, biochar, and lime + microbial fertilizer were added to soil, and bare land was set as the control (CK). High throughput sequencing technology (Illumina MiSeq) was used to study the effects of the three fertility improvement measures on bacterial and fungal community structures. 【Result】Results showed that 21 bacteriophyta and 7 mycobionta were detected in biological soil crusts. The dominant bacteriophyta were Acidobacteria (27.39%), Proteobacteria (25.90%), Actinobacteria (16.68%), Chloroflexi (12.26%), while the dominant mycobionta were Basidiomycota (61.19%) and Ascomycota (29.48%). The three fertility improvement measures had no significant effects on the diversities of bacteria and fungi, but significantly changed their community structures in order of organic fertilizer > biochar > lime + microbial fertilizer, and these effects were higher in bacteria, compared to fungi. Also, the effects of the three fertility improvement measures on specific bacteriophyta and mycobionta were different. The three fertility improvement measures increased the relative abundance of Proteobacteria, and decreased the relative abundance of Chloroflexi. Organic fertilizer and lime + microbial fertilizer increased the relative abundance of Ascomycota, but decreased the relative abundance of Basidiomycota, while biochar had opposite effects on mycobionta. Among the soil environmental factors, pH, organic carbon, and total nitrogen had a great influence on microbial community structure.【Conclusion】These results provided significant scientific guidance for the regulation of soil microbial community structures in biological soil crusts, which is beneficial for the formation of biological soil crusts and the control of water and soil erosion in southern red soil.