The objectives of this research were to analyze anthocyanins in blue honeysuckle (Lonicera caerulea L.), bilberry (Vaccinium vitis-idaea L), and cranberry (Vaccinium macrocarpon Ait.), using HPLC-ESI-QTOF-MS2, Fourteen, fifteen, and eight anthocyanins were identified in blue honeysuckle, bilberry, and cranberry, respectively. Cyanidin-3-glucoside (C3G) and peonidin-3-glucoside were detected in all three types of berries, with blue honeysuckle showing the highest C3G content at 5686.28 mg/100 g DW. Total phenolic content (TPC) and total flavonoid content (TFC), along with ABTS, DPPH, and FRAP assays, were measured. Blue honeysuckle exhibited the highest levels of TPC and TFC. The SOD, POD, and CAT activities in blue honeysuckle were 1761.17 U/g, 45,525.65 U/g, and 1043.24 U/g, respectively, which were significantly superior to those in bilberry and cranberry. The antioxidant mechanisms of these enzymes were investigated by molecular docking, C3G showed a higher affinity for POD, confirming the effectiveness of C3G as an antioxidant.