In order to reduce the nitrogen dosage of citrus fertilizer and promote the sustainable development of orange orchard，the influence of organic fertilizer replacement on citrus fruit quality，soil nutrients，microbial activity and bacterial community was carried out. The experiment adopted a one-factor randomized block design. Four treatments of organic fertilizers substituting chemical fertilizer were set up：0（CK），25% substitution（T1），50% substitution（T2）and 75% substitution（T3）. During the ripening period，soil was sampled to determine soil nutrients，fruit quality，soil enzyme activity，soil bacterial communities，and citrus CO₂ flux throughout the year. The application of organic fertilizer significantly improved the soil fast nutrients and thus improved the fruit weight，vitamin C and soluble solids. The replacement of chemical fertilizer with organic fertilizer improved soil microbial activity and improved soil CO₂ emission flux. The application of organic fertilizer significantly improved the activity of soilβ-glucosidase（BG）and acid phosphatase（AP），and significantly reduced the activity of leucine aminopeptidase（LAP）. The replacement of chemical fertilizer with organic fertilizer significantly increased the diversity of soil bacterial community and improved the relative abundance of soil bacteria such as Rhoplankton and Bacillus. The results of RDA analysis showed that the replacement of organic fertilizer affected the soil bacterial community，among which the effective phosphorus，organic matter，pH and effective magnesium were the key factors affecting the bacterial community in this experiment. Organic fertilizer replacement significantly improved the soil microbial activity，activated the soil quick nutrients，increased the relative abundance of beneficial bacteria，played an important role in citrus healthy growth. Organic fertilizer replacing 50% of chemical fertilizer in base fertilizer had the best effect on improving soil available nutrients and citrus quality，compared with CK，it significantly increased citrus fruit weight by 34.58%，transverse diameter by 14.02%，longitudinal diameter by 15.21%，soluble solid content by 25.43% and vitamin C content by 16.46%. The results can provide reference for the rational replacement of organic fertilizer in citrus orchard， improve the quality of citrus and promote the sustainable development of orange orchard.