To comprehensively evaluate the physicochemical characteristics and bioactivities of three distinctive Apis cerana (A. cerana) honeys—Bauhinia championii honey (BCH), Polygonum perfoliatum honey (PPH), and Rhus chinensis honey (RCH)—systematic analyses were performed on total phenolic content (TPC), in vitro antioxidant capacity (via DPPH, ABTS, and FRAP assays), antibacterial efficacy against Staphylococcus aureus (S. aureus) and Escherichia coli, and volatile composition analysis. Among the varieties, BCH presented the most substantial TPC (636.21 ± 17.05 mg GAE/kg), a value statistically higher than that of PPH and RCH (p < 0.05), and correspondingly exhibited superior antioxidant performance across all assays. All honeys displayed a clear concentration-dependent antioxidant effect. Antibacterial assays revealed that both undiluted and diluted (0.5 g/mL) samples exerted significant inhibitory effects on the tested pathogens, furthermore, BCH and PPH showing significantly higher inhibition against S. aureus than the positive control (penicillin, p < 0.05). Volatile profiling by HS-SPME-GC-QQQ identified 42, 35, and 38 volatile compounds in BCH, PPH, and RCH, respectively, including esters, terpenes, aldehydes, and phenolics. Cedrol (in PPH), phenylethyl acetate (in BCH), and benzaldehyde (in RCH) were pinpointed as potential botanical markers that define their characteristic aroma profiles and may partially contribute to their bioactivity. Collectively, these honeys possess remarkable antioxidant and antibacterial properties, with BCH showing the greatest potential for functional food applications owing to its high phenolic concentration and robust overall bioactivity. These findings elucidate the intrinsic link between the botanical chemical signatures of A. cerana honey and its biological functions, offering a scientific foundation for their utilization in functional food innovation, geographical indication protection, and quality authentication.