In order to explore the impact of biochar and green manure on the micro-ecological environment of citrus soil, a field experiment was used to set CK (conventional fertilization), T1 (5.0 kg/biochar) and T2 (5.0 kg/biochar + 10% nitrogen fertilizer reduction + green manure), for measuring the 3 kinds of fertilization affectness to the fungal diversity and community structure of citrus rhizosphere soil. The results showed that, compared with CK, the pH, alkali-hydrolyzable nitrogen, available phosphorus and available potassium content of T1 and T2 treatments were significantly increased, and soil bulk density was significantly reduced. Application of only biochar increased the diversity of soil fungi, but reduced the richness of fungi. Combined application of biochar and green manure significantly increased the diversity and richness of fungi. Application of biochar increased the relative abundance of Basidiomycota, Schizoplasmodiida, and Talaromyces in soil, and decreased relative abundance of Ascomycota, Mucoromycota, Chaetomium and Fusarium. The study shows that the combined application of biochar and green manure can significantly increase the soil fungal diversity, reconstruct community structure of soil fungi, reduce the abundance of pathogenic bacteria, and promote micro-ecological balance in soil for citrus and soil health。