The honeycomb composition is very complex, containing honey, royal jelly, pollen, and propolis, and thus contains a large number of bioactive ingredients, such as polyphenols and flavonoids. In recent years, honeycomb as a new functional food resource has been favored by many bee product companies, but the basic research on honeycomb is lacking. The aim of this study is to reveal the chemical differences between A. cerana honeycombs (ACC) and A. mellifera honeycombs (AMC). In this paper, we studied the volatile organic components (VOCs) of ACC and AMC by solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS). A total of 114 VOCs were identified in 10 honeycombs. Furthermore, principal component analysis (PCA) revealed that the chemical composition of ACC and AMC were different. Additionally, orthogonal partial least squares discrimination analysis (OPLS-DA) revealed that benzaldehyde, octanal, limonene, ocimene, linalool, α-terpineol, and decanal are the significant VOCs in AMC extracts, which are mainly derived from propolis. OPLS-DA model also identified 2-phenylethanol, phenethyl acetate, isophorone, 4-oxoisophorone, betula, ethyl phenylacetate, ethyl palmitate, and dihydrooxophorone as potential discriminatory markers of ACC, which likely contribute to protecting the hive against microorganisms and keep it clean.