The chemical composition and quality of honey are influenced by its botanical, geographic, and entomological origins, as well as climatic conditions. In this study, the physicochemical characteristics, microbial communities, and hydrocarbon compounds of honey produced by Apis mellifera, Apis cerana, Apis laboriosa, Apis dorsata, and Apis florea were elucidated. The physicochemical profile of the honey exhibited significant differences across species, including moisture content (18.27%–23.66%), fructose (33.79%–38.70%), maltose (1.10%–1.93%), electrical conductivity (0.37–0.74 mS/cm), pH (3.36–3.72), diastase activity (4.50–29.97 diastase number), and color (37.90–102.47 mm). Microbial analysis revealed a significant abundance of lactic acid bacteria, particularly the Apilactobacillus genus in A. laboriosa honey and the Lactobacillus in A. florea honey, indicating significant probiotic potential. Chemometric methods, principal component analysis, hierarchical cluster analysis, and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to classify the honey samples based on the 12 beeswax-derived hydrocarbons. The OPLS-DA model demonstrated 100% accuracy in predicting the entomological origin of honey, indicating that specific hydrocarbons are reliable markers for honey classification.