Abstract: To address the issues of soil quality degradation and declining fruit quality in Citrus reticulata cv. Shatangju, a field experiment was conducted in Yunfu City, Guangdong Province. The experiment comprised three treatments: organic fertilizer combined with soil conditioner and microbial fertilizer (T_A), organic fertilizer combined with soil conditioner (T_B), and organic fertilizer combined with microbial fertilizer (T_C), with organic fertilizer alone as the control (CK). After one year of the experiment, soil physicochemical properties, microbial community structure, and Citrus reticulata cv. Shatangju fruit quality were analyzed to identify the optimal fertilization strategy for soil improvement and fruit quality enhancement. The results indicated that T_A exhibited the best overall soil improvement effects. Compared with CK, T_A significantly increased the abundance of soil bacteria, Actinomycetes, and total microorganisms by 80.4%, 73.4%, and 78.9%, respectively. However, the ratio of Gram-negative to Gram-positive bacteria was significantly reduced by 18.9% under T_A. In addition to improving soil parameters, T_A also significantly enhanced the yield and quality of Citrus reticulata cv. Shatangju. Specifically, compared with CK, T_A significantly increased single-fruit weight, yield per plant, and the contents of total soluble sugars, vitamin C, and soluble solids by 23.0%, 35.4%, 10.8%, 5.60%, and 10.9%, respectively, while the titratable acid content decreased by 3.45%. The combined application of organic fertilizer, soil conditioner, and microbial fertilizer effectively improved soil physicochemical properties and microbial community structure in Citrus reticulata cv. Shatangju, and enhanced fruit yield and quality, representing a promising strategy for soil amelioration and fruit quality improvement.