The overexpression of anaplastic lymphoma kinase (ALK) had been found in many types of cancers, especially the non-small-cell lung cancers (NSCLCs). So the discovery of novel ALK inhibitor had attracted a great deal of interest in anticancer drugs research area. Presently, a combined study of 3D-quantitative structure-activity relationship (3DQSAR) and molecular docking was undertaken to explore the structural insights of 36 2-acyliminobenzimidazoles compounds influencing the ALK inhibitory activities. Both the ligand-based resultant comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models exhibited good predictability (CoMFA with R2, 0.995; q2, 0.534; CoMSIA with R2, 0.993; q2, 0.519;). 3D contour maps and docking results suggested different groups on the core parts of the componds could enhance the biological activities. Finally, 10 derivatives as potential candidates of ALK inhibitors with excellent predicted activities were designed.