To mitigate the issues of soil quality degradation and environmental pollution caused by excessive fertilizer use in apple orchards, the present study investigated the effects of organic fertilizer substitution combined with chemical nitrogen (N) fertilizer reduction on soil nutrient status, enzyme activity, and microbial communities (bacteria, fungi and archaea) over one year in an apple orchard. Five fertilization treatments were implemented, including 100% chemical fertilizer (CK), 80% chemical fertilizer + 20% liquid humic fertilizer (S1), 60% chemical fertilizer + 40% liquid humic fertilizer (S2), 60% chemical fertilizer + 20% liquid humic fertilizer (S3), and 40% chemical fertilizer + 40% liquid humic fertilizer (S4). Substituting chemical fertilizers with liquid humic fertilizers effectively enhanced the soil organic matter (SOM) content in the topsoil (0–20 cm) for all treatments. Compared to CK, the amounts of available N (NO3−-N and NH4+-N) were decreased in the topsoil and the amounts of total N, total phosphorous and available phosphorous were increased in the subsoil (20–40 cm) for all treatments. The β-diversity of bacterial communities exhibited the highest sensitivity to soil environmental changes, followed by that of archaea, whereas fungi demonstrated the least susceptibility. The higher soil carbon/nitrogen ratio and SOM content in S2 altered the abundance of microorganisms (Proteobacteria, Ascomycota, and Crenarchaeota) that were closely related to the decomposition and mineralization of SOM and N, enhancing the efficiency of SOM decomposition. The activities of sucrase (SUC), urease (UE), and phosphatase were increased, also promoting the conversion efficiency of SOM and improving N fixation and soil fertility. In the organic fertilizer substitution treatments (S1 and S2), the abundance of dominant Actinobacteriota, Ascomycota and Crenarchaeota phyla were increased, as well as the activities of SUC and UE, accelerating the decomposition and mineralization of SOM and improving soil fertility. In the top, organic fertilizer substitution combined with reduced chemical N fertilizer (S3 and S4) treatments increased the abundance of bacteria and fungi. In addition, RDA showed that total potassium content could significantly affect changes in the bacterial and fungal community structure in subsoil. Overall, organic fertilizer substitution enhanced the content of soil available nutrients and improved soil nutrient retention. It is recommended to promote organic fertilizer substitution + chemical N fertilizer reduction (S4) with the supplementation of potassium fertilizer in the subsoil. The findings provide a theoretical basis and practical guidance for improving orchard soil management and achieving sustainable development in the apple industry.