The development of physiologically active semiochemicals is largely limited by the labor-consuming searching process. How to screen active semiochemicals efficiently is of significance to the extension of behavior regulation in pest control. Here pharmacophore modeling and shape-based virtual screening were combined to predict candidate ligands for Cydia pomonella pheromone binding protein 1 (CpomPBP1). Out of the predicted compounds, ETrME displayed the highest affinity to CpomPBP1. Further studies on the interaction between CpomPBP1 and ETrME, not only depicted the binding mode, but also revealed residues providing negative and positive contributions to the ETrME binding. Moreover, key residues involved in interacting with ETrME of CpomPBP1 were determined as well. These findings were significant to providing insights for the future searching and optimization of active semiochemicals.