Forsythia suspensa (Thunb.) Vahl (FS) is an important plant with high edible and medicinal values. The edible fruit of FS is a common traditional medicine in China, Japan and Korea. Compared to the research on the phytochemistry and pharmacology of the fruits, study on the other parts of FS, such as leaves and flowers is still limited. In this study, an integrated strategy based on ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS/MS), plant metabolomics and correlation analysis was established for comprehensively chemical characterization of fruits, leaves and flowers of FS, and discovery of α-glucosidase and pancreatic lipase inhibitory metabolites. The plant metabolic profiling of fruits, leaves and flowers of FS was performed by UPLC-QTOF-MS/MS, and a total of 74 secondary metabolites, including 15 phenylethanoid glycosides, 20 lignans, 10 cyclohexanol derivatives, 11 organic acids, 9 flavonoids, 3 triterpenes, and 10 other compounds were identified. Then, 29 differential secondary metabolites that responsible to distinguish the fruits, leaves and flowers of FS were further screened out by multivariate statistical analysis. Meanwhile, the α-glucosidase and pancreatic lipase inhibition of different parts of FS were evaluated and compared by in vitro experiments. The results demonstrated that the leaves of FS showed the highest inhibition on α-glucosidase and pancreatic lipase with IC50 of 0.17 ± 0.04 mg/mL and 0.56 ± 0.33 mg/mL, respectively. Then, the correlation between differential metabolites and enzyme inhibitory activities were investigated by Pearson correlation analysis, and 12 potential α-glucosidase and pancreatic lipase inhibitors were screen out. Additionally, the α-glucosidase and pancreatic lipase inhibitory activities of five potential enzyme inhibitory components, including quercitrin, rutin, kaempferol-3-O-rutinoside, pinoresinol-4-O-glucoside and phillyrin were further validated by in vitro assays and molecular docking analysis. The results showed that all the five potential inhibitors showed good inhibitory effects on α-glucosidase and pancreatic lipase, and the binding of the five inhibitors to enzymes mainly through hydrogen bonding, hydrophobic force, and ionic bonding. This study provided a feasible strategy for comparison and discrimination of different parts of medicinal plant and discovery of bioactive components, and also provided useful information for future utilization of different parts of FS.