Lonicera japonica Thunb. and Lonicera hypoglauca are famous Chinese medicines used for hyperglycemia; however, the specific compounds that contributed to the hypoglycemic activity and mechanism are still unknown. In this study, the antidiabetic activity of L. japonica buds and L. hypoglauca buds, roots, stems, and leaves extracts was primarily evaluated, and the L. japonica buds and L. hypoglauca buds, roots, and stems extracts displayed significant hypoglycemic activity, especially for the buds of L. hypoglauca. A total of 72 high-level compounds, including 9 iridoid glycosides, 12 flavonoids, 34 organic acids, and 17 saponins, were identified by ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) combined with the fragmentation pathways of standards from different parts of L. japonica and L. hypoglauca extracts. Among them, 19 metabolites, including 13 saponins, were reported for the first time from both medicines. Seven high-content compounds identified from L. hypoglauca buds extract were further evaluated for hypoglycemic activity. The result indicated that neochlorogenic acid, chlorogenic acid, isochlorogenic acid A, isochlorogenic acid B, and isochlorogenic acid C displayed significant antidiabetic activity, especially for isochlorogenic acid A and isochlorogenic acid C, which demonstrated that the five chlorogenic-acid-type compounds were the active ingredients of hypoglycemic activity for L. japonica and L. hypoglauca. The potential mechanism of hypoglycemic activity for isochlorogenic acid A and isochlorogenic acid C was inhibiting the intestinal α-glucosidase activity to block the supply of glucose. This study was the first to clarify the hypoglycemic active ingredients and potential mechanism of L. japonica and L. hypoglauca, providing new insights for the comprehensive utilization of both resources and the development of hypoglycemic drugs.