Honey is a complex food product, and has been linked to a number of substantial health advantages. The aim of this study was to assess the phenolic compounds, organic acids, microbial community, antioxidant activity, and antimicrobial activity of multifloral honeys produced by Apis cerana cerana, A. dorsata, and Lepidotrigona flavibasis in Hainan province, China. Our results illustrated that chlorogenic acid was the major phenolic component in all honeys. L. flavibasis honey showed the greatest antioxidant activity (DPPH IC50 value, 7.66 mg/mL; FRAP value, 5217.06 µmol TE/kg), as well as the highest levels of proline (548.64 mg/kg), total flavonoid (11.67 mg QE/100 g), total phenolic (132.73 mg GAE/100 g), and Lactobacillus (96.28 %). Besides, all honeys were found to have a broad spectrum of antibacterial activity. Overall, our data imply that Hainan honeys, particularly stingless bee honeys, have been beneficial components of human diets.