At present, studies on the application of biochar in citrus production are rare and unsystematic. Our research systematically explored the effects of biochar on citrus quality, soil nutrient status, heavy metal environment, and microbial communities in citrus production. This experiment set up four treatments: no biochar (CK), 5 kg/plant biochar (B5), 10 kg/plant biochar (B10), and 15 kg/plant biochar (B15) and analyzed two soil layers (0–20 cm, 20–40 cm). The results indicated that citrus fruit indexes (peel, edibility, soluble solid-to-titratable acidity ratio, soluble solids) and soil physicochemical properties (pH, organic matter, nutrient elements) had positive response to biochar application. In terms of microorganisms, biochar significantly improved the richness, evenness, and diversity of soil bacteria, but reduced the evenness of fungi. All biochar treatments led to the enrichment of beneficial bacteria. Simultaneously, saprophytic fungi that can promote nutrient cycling were significantly enriched after the application of biochar. Comprehensive analysis of all indicators showed that 10 kg/plant treatment was the most suitable proportion for promotion in citrus production. In general, this research from multiple angles demonstrated that the application of biochar in citrus production could be profitable and sustainable.