Soil fungi are essential for nutrient cycling and sustainable farming, yet their responses to organic amendments in semi-arid Astragalus systems remain unclear. We investigated the impact of manure (MF) and compost (CF) fertilization on soil properties and fungal communities over two years, analyzing 36 soil samples collected from two depths (0-20 cm and 20-50 cm). Fungal communities were assessed through high-throughput ITS sequencing, and their relationships with soil properties were explored using network analysis, redundancy analysis (RDA), multiple linear regression, and random forest models. Both MF and CF significantly (p < 0.05) improved soil properties, raising the soil quality index (SQI) from 0.18 in the control (CK) to 0.50 with CF and 0.55 with MF. Soil traits and fungal abundance decreased with depth, with topsoil favoring symbiotrophs and subsoil favoring saprotrophs and pathotrophs. Organic amendments increased saprotrophic fungi (MF: 87.26 %; CF: 52.37 %) compared to CK (47.03 %), and reduced pathotrophs (MF: 9.43 % vs. CK: 29.38 %). Ascomycota and Basidiomycota were positively correlated with SOC, NO3--N, and AP, highlighting their roles in nutrient cycling. Network analysis revealed higher modularity under MF (0.609) and CF (0.625) compared to CK (0.555), indicating stronger fungal associations and greater microbial resilience. These results demonstrate that manure and compost not only improve soil quality and the complexity of fungal networks but also shift fungal guilds toward decomposers. These findings suggest that incorporating organic amendments, such as manure and compost, instead of chemical fertilizers can enhance soil quality and support sustainable agriculture in semi-arid farming systems.