To investigate the effects of biochar-based microbial fertilizer on soil and apple ［Malus domestica (Suckow) Borkh.］ trees in orchards, a field randomized block experiment was conducted in the orchard of Xudikou Village, Fengxian County, Xuzhou City, Jiangsu Province, and the differences in soil physicochemical properties and biological characteristics, as well as flower number per branch, new shoot growth, fruit yield, and fruit quality of apple trees, were compared under four treatments, namely no fertilization (CK), conventional fertilizer (CF), 30% reduction of fertilizer combined with biochar (CF-30+BC), and 30% reduction of fertilizer combined with biochar-based microbial fertilizer (CF-30+BMF), and the Pearson correlations between the relevant indexes of apple trees and soil were analyzed. The results show that, overall, compared with the CK and CF groups, soil organic matter content, total nitrogen content, total phosphorus content, total potassium content, alkali-hydrolyzable nitrogen content, available phosphorus content, available potassium content, sucrase activity, urease activity, and alkaline phosphatase activity significantly increase (P<0.05) in the CF-30+BC and CF-30+BMF groups, and the flower number per branch, new shoot growth, fruit yield, and most fruit quality indexes of apple trees also significantly increase. Moreover, the increments in indexes of soil and apple trees are greater in the CF-30+BMF group, and the alkali-hydrolyzable nitrogen content, available phosphorus content, available potassium content, sucrase activity, urease activity, alkaline phosphatase activity of soil, as well as the flower number per branch, new shoot growth, fruit coloration index, vitamin C content, and soluble sugar content of apple trees in this group are all significantly higher than those in the CF-30+BC group. The correlation analysis result shows that fruit yield has significant positive correlations with soil organic matter content, sucrase activity, and urease activity, fruit soluble sugar content has significant positive correlations with soil total nitrogen content, alkali-hydrolyzable nitrogen content, available phosphorus content, urease activity, and alkaline phosphatase activity, while correlations between the other fruit quality indexes and soil indexes are mostly non-significant. In conclusion, under the condition of 30% reduction of fertilizer, both biochar and biochar-based microbial fertilizer application can significantly improve orchard soil fertility, increase flower number and new shoot growth of apple trees, thereby enhance fruit yield and quality, achieving the goal of reducing fertilizer input and increasing efficiency.