This study aims to investigate the polyphenols extraction rate of various methods from Mesona chinensis Benth, compare the differences of glucose consumption in insulin-resistant HepG2 cells in the effect of polyphenols extracted by these methods, analysis the hub genes and main metabolic pathways involved in the hypoglycemic effect of M. chinensis polyphenols. Five extraction methods, including water extraction (Wat), ethanol extraction (Eth), ultrasound-assisted extraction (Ult), microwave-assisted extraction (Mic), and enzymatic extraction (Enz), were employed to extract polyphenols from M. chinensis. An insulin-resistant model was established using HepG2 cells to compare the effects of polyphenols extracted by different methods on glucose consumption and to select the optimal extraction method. Further, the insulin-resistant HepG2 cell model was treated with M. chinensis polyphenols obtained by the optimal extraction method and metformin hydrochloride separately, followed by high-throughput sequencing to screen for differentially expressed genes. KEGG pathway enrichment analysis was conducted, and a protein-protein interaction (PPI) network was constructed to further identify hub genes. The results indicated that the Wat had the highest extraction rate for M. chinensis polyphenols, followed by the Enz, while the Mic had the lowest rate. However, the polyphenols extracted by Enz demonstrated the best effect on promoting glucose consumption in insulin-resistant model cells at a concentration of 0.06 mg/mL, which was 36.36% higher than that of metformin hydrochloride control group. Through the construction of PPI network, 12 hub genes related to glucose consumption in diabetes were identified, among which ATF3, ACSS2, ASNS, and INSIG1 have not been reported in specific regulatory mechanisms or treatment of diabetes at present. KEGG pathway enrichment analysis revealed that M. chinensis polyphenols were involved in multiple signaling pathways related to blood glucose regulation or insulin sensitivity regulation. In summary, M. chinensis polyphenols exhibited significant hypoglycemic effects. The discovery of the hub genes and signaling pathways not only provided a new target for blood glucose regulation, offered data support and theoretical basis for the development of natural, safe and efficient hypoglycemic drugs, but also presented a perspective for the study of the related mechanisms of diabetes occurrence or treatment.