Soil microbial carbon (C), nitrogen (N), and phosphorus (P) nutrient requirements and metabolic limitations are closely related to the availability of environmental nutrients. However, it is unclear how manure and chemical fertilization shift nutrient limitations for microbes in terms of the soil enzymatic stoichiometry in an apple orchard. Therefore, based on the long-term experiment located in an apple orchard established in 2008, this study applied the theory and method of soil enzyme stoichiometry to systematically investigate the effects of the combined application of manure and chemical fertilizers on soil C, N, and P turnover-related enzyme activities (β-1,4-glucosidase, BG; leucine aminopeptidase, NAG; β-1,4-N-acetylglucosaminidase, LAP; and acid or alkaline phosphatase, PHOS) and their stoichiometric characteristics and analyzed their relationships with environmental factors and microbial carbon use efficiency. The experiment was designed with four treatments, such as, no fertilization input as the control (CK), single application of chemical fertilizer (NPK), combined application of manure and chemical fertilizer (MNPK), and single application of manure (M). The results revealed that:① at different growth stages of fruit trees, the soil microbial biomass C (microC) content of manure fertilizer treatments (MNPK and M) was significantly higher than that of no manure fertilizer treatments (CK and NPK). The content of microbial biomass N (microN) in the NPK, MNPK, and M treatments increased by 89%, 269%, and 213%, respectively, compared with that in CK (P<0.05). ② Compared with those in the fertilization treatments, CK had higher leaf N and P contents (29.8 g·kg-1 and 2.17 g·kg-1) at the germination stage, and the leaf P content at the germination stage alone was significantly negatively correlated with soil available phosphorus (AP) content. ③ Soil enzyme stoichiometry analysis demonstrated that all data points in this study were above the 1:1 line, indicating that microbial communities had a strong phosphorus limitation. The range of vector length and angle was 0.56-0.79 and 59.3°-67.7°, respectively, in the growth period of fruit trees, and the vector angle was >45° in this study, which also reflected the strong phosphorus limitation of microorganisms. ④ RDA and random forest model analysis showed that organic carbon and available nitrogen (AN) were the main physical and chemical factors affecting vector length; AP, AN, and soil water content were the main physical and chemical factors affecting vector angle. Combined with SEM analysis, AN and dissolved organic carbon (DOC) directly affected microC and microN, AP directly affected microP and microN, DOC and AP directly affected vector length, and AP and microN directly affected vector angle. In addition, microbial carbon utilization was positively correlated with vector length and negatively correlated with vector angle. In summary, the combined application of manure and chemical fertilizers regulated microbial carbon and phosphorus metabolism by affecting soil carbon and phosphorus content at different growth stages of fruit trees, thereby affecting microbial carbon utilization. This study provides a scientific basis for manure and chemical fertilizers to improve soil quality and maintain soil health.