[Objective] This study investigated the optimal proportion of green manure replacing chemical fertilizer and its effect on soil fungal community in the paddy field of Ultisol, aiming to achieve soil fertilization and sustainable utilization of Ultisol in southern China. [Methods] This study set seven treatments: no fertilizer (Control), application of Chinese milk vetch without chemical fertilizer in early season rice (G), conventional application of chemical fertilizer in early season rice (NPK100), application of Chinese milk vetch and conventional chemical fertilizer in early season rice (NPK100+G), application of Chinese milk vetch and 80% conventional chemical fertilizer in early season rice (NPK80+G), application of Chinese milk vetch and 60% conventional chemical fertilizer in early season rice (NPK60+G), and application of Chinese milk vetch and 40% conventional chemical fertilizer in early season rice (NPK40+G). The conventional chemical fertilizer was applied in late season rice for other treatments except the Control. The root surface soil samples of different treatments were collected at the maturity stage of late rice for the measurement of soil properties. At the same time, high-throughput sequencing (Illumina MiSeq) was employed to analyze the features of soil fungal community. [Results] Compared with NPK100, the treatments of green manure replacing chemical fertilizer increased the yields of rice and straw. Different treatments significantly altered the soil fungal community composition (P=0.001). Replacing medium and low amounts of chemical fertilizer with green manure increased the relative abundance of saprophytic fungi in soil, which increased the conversion rate of soil organic matter and nutrient turnover rate. Compared with NPK100, replacing 0, 20%, and 40% chemical fertilizer with green manure increased the relative abundance of saprophytic fungi in soil by 33.55%, 167.27%, and 55.28%, respectively. In addition, replacing medium and low amounts of chemical fertilizer with green manure decreased the relative abundance and diversity of potential plant pathogens in soil. [Conclusion] Replacing medium and low amounts (20%–40%) of chemical fertilizer with green manure not only increased rice yield but also reduced environmental pollution, improved soil nutrients, and optimized the fungal community in soil. This study systematically evaluated the effect of replacing different proportions of chemical fertilizer with green manure on the Ultisol paddy ecosystems. The results provided a theoretical basis for the sustainable development of agriculture in the Ultisol region of southern China.