Soil microbial communities play an essential role in maintaining soil fertility and are considered as ecological indicators to evaluate soil health. In the present study, we examined the influence of almost 4 years of fertilization [no fertilizer (CK), nitrogen alone (N), nitrogen, phos-phorus and potassium chemical fertilizer (NPK), organic manure (M), nitrogen plus organic manure (NM), and NPK plus organic manure (NPKM)] on soil fertility and the functional diversity of soil microbial communities in an apple orchard. Compared to CK, fertilization increased soil organic carbon, total nitrogen, and available nutrients, but reduced soil pH in N and NPK treatments. The highest microbial biomass carbon and nitrogen, most probable number of actinomycetes, bacteria, and fungi occurred in the NPKM treatment. The average well color development (AWCD) values followed the order of NPKM > M> NPK and NM > CK and N. The Shannon index in organic manure treatments were signifi-cantly higher than in control and in treatments without organic manure. The principal component analysis showed that manure treatment was significantly separated from other treatments. These results indicated that organic manure applied alone or in combination with chemical fertilizers would increase soil fertility and functional diversity of soil microbial communities. Moreover, applying balanced N, P, K fertilizer in combination with organic manure was found to be superior to the use of a single fertilizer in improving soil microbial community quality.