In this study, 3D-QSAR pharmacophore models were used to screen Chrysin (Chr), Genistein (Gen) and Naringenin (Nar) as inhibitors of pancreatic lipase (PL). The mechanisms of inhibition were explored using PL activity assays, enzyme kinetics, multispectral techniques, molecular docking, and molecular dynamics (MD) simulations, leading to the construction of a pharmacophore model that included two hydrogen bond acceptors and one hydrophobic group. Chr, Gen, and Nar competitively and reversibly inhibited PL with IC₅₀ values of 22.98?±?1.45, 42.36?±?0.35, and 48.66?±?0.25?μmol·L^?1, respectively, and inhibition constants of (6.2995?±?0.01)?×?10^?5, (6.5494?±?0.02)?×?10^?5 and (2.4361?±?0.02)?×?10^?5?mol·L^?1, respectively. Kinetic analysis, fluorescence quenching assays and molecular docking showed that thee compounds interacted with PL close to its active site (Ser153-His264-Asp177), affecting the microenvironment of tryptophan residues, and bound stably to PL via hydrogen bonds, hydrophobic interactions, and van der Waals forces. UV–visible spectra showed binding constants of 65.40?×?10³, 62.70?×?10³ and 6.41?×?10³?L/mol, respectively. MD simulations indicated that the structures of the complexes were compact, with binding free energy analysis ranking the PL inhibitory abilities of the compounds as Chr?>?Gen?>?Nar. In summary, the pharmacophore model was accurate. Chr, Gen, and Nar could inhibit PL activity. These findings provide a reference for the screening and development of new PL inhibitors.