Abstract: Soil micro-organisms constitute a significant part of soil fertility and play a critical role in maintaining soil ecological functions. Micro-organisms also are key indicators for soil quality and productivity. No-tillage and mulching cultivation indirectly affect the composition of soil microbial community by changing plant physiological characteristics and root exudates. The two agronomic practices can also improve soil environment by increasing the total amount of micro-organisms in the soil. By analyzing the composition of soil microbial community under no-tillage, mulching and organic cultivation of winter wheat in the southern mountain areas of Ningxia, the effects of agricultural management activities on soil microbial community structure and arbuscular mycorrhizal (AM) fungal diversity were determined in this paper. The study aimed at providing theoretical basis for the promotion of long-term no-tillage, mulching cultivation, sustainable use of farmlands and maintenance of soil microbial diversity. Short-term test on conservation tillage (no-tillage) was done for three consecutive years in Longde County, Guyuan. Four soil treatments were selected including no-tillage and straw mulching without organic fertilizer application (NC), no-tillage and straw mulching with organic fertilizer application (NF), traditional tillage and no-mulching without organic fertilizer application (TC) and traditional tillage and no-mulching with organic fertilizer application (TF). By using Illumina Miseq high-throughput sequencing platform and phospholipid fatty acids (PLFAs) analysis methods, soil microbial community composition, AM fungi community composition and diversity and soil environmental factors were analyzed after three years cultivation of winter wheat. The results showed that continuous no-tillage, mulching and organic fertilizer application increased soil microbial community biomass characterized by PLFA. Traditional tillages significantly improved microbial community biomass (P < 0.05) of gram-positive (G⁺) and negative (G^-) bacteria in the soil. With increasing years of management of no-tillage and straw mulching, soil AM fungi biomass significantly increased. Also biomass ratios of 16:1ω5c neutral lipid (NLFA) to 16:1ω5c phospholipid lipid (PLFA) significantly increased (P < 0.05). Under no-tillage and straw mulching, the application of organic fertilizer increased soil AM fungi richness index (Chao1 index and ACE index), but reduced soil AM fungi diversity (Shannon index and Simpson index). The results of principal component analysis showed that biomass of AM fungal spores (16:1ω5 c neutral fat) was positively correlated with soil contents of organic matter, and easily extracted glomalin. While AM fungi richness index was positively correlated with soil organic matter content, AM fungi diversity index was positively correlated with soil total nitrogen content and urease activity. AM fungi richness and diversity were affected by soil physical and chemical properties and soil biological differences. Also soil microbial biomass changed along with AM fungal diversity and richness. It was concluded that no-tillage and straw mulching cultivation increased soil AM fungi diversity. The proportion of NLFA to PLFA biomass of AM fungi was also significantly affected by the application of organic fertilizer, and changed distribution of biomass carbon between AM fungi spores and mycelium.