A 3D-CoMFA model with pranlukast analogues was constructed, which could be applied to predict the antagonistic activity of aryl benzyl ether analogues against LTD4. Molecular modeling and 3D-CoMFA studies were performed on 78 pranlukast analogues and 14 aryl benzyl ethers to evaluate the antagonistic behavior of aryl benzyl ethers and provide information for further modification of this kind of compounds. The aryl benzyl ether core was found to be in excellent three dimensional match with the central planar moiety of pranlukast analogues, and the pranlukast 3D-CoMFA model could be successfully applied to predict the biological activity of aryl benzyl ether analogues.