To understand pharmacophore properties of Pyrimidine-Benzimidazole hybrids derivatives and to design novel inhibitors of Serin protease, GQSAR approach was applied to analyze Group quantitative structure-activity relationship of 17 compounds. AutoDock 4.0 program was employed to locate the orientations and conformations of the inhibitors interacting with Serin protease. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding, and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive G-QSAR model was obtained by R2 with Q2 values of 0.9865 and 0.9405 for cross-validated respectively. The G-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyrimidine-Benzimidazole hybrids derivatives against Serin protease.