The discovery of effective and targeted drugs remains a challenge in modern drug development due to issues such as drug resistance and off-target effects. Traditional screening methods are often limited by precise identification of active compounds and lack of efficiency for screening. Integrated approaches are necessary to improve the efficiency of the screening process of drug discovery. Based on our previous studies, the extract of leaves of Morus alba L. exhibited a promising inhibition effect on protein tyrosine phosphatase 1B (PTP1B). Thus, the aim of this study was to recognize, characterize and evaluate the bioactive compounds in M. alba L. acting on PTP1B. A PTP1B affinity chromatography column was constructed to capture the compounds binding on PTP1B from M. alba L. Meanwhile, the constructed PTP1B column was characterized in terms of functional activity, particle morphology, and selectivity profile. Subsequently, the captured compounds were annotated by liquid chromatography coupled with mass spectrometry, as chlorogenic acid, rutin, mulberrofuran G, sanggenon C, and astragalin. In addition, their inhibition effects were assessed by the determination of IC50 values on PTP1B. The IC50 values were 2.66 x 103 ± 0.24 × 103 μM for chlorogenic acid, 660.45 ± 134.33 μM for rutin, 17.17 ± 0.30 μM for mulberrofuran G, 13.38 ± 0.22 μM for sanggenon C, and 192.96 ± 66.46 μM for astragalin, respectively. Molecular docking was performed to explore their binding mechanisms. In summary, this study established an effective affinity chromatography setup for PTP1B inhibitors screening. Furthermore, mulberrofuran G and sanggenon C were identified as potential PTP1B inhibitors.