Background: ALK was a receptor tyrosine kinase (RTK) belonging to the insulin receptor superfamily. Many ALK fusion partner genes have been identified in NSCLC, such as NPM, EML4, TFG, KLC1, KIF5B and PTPN3. There had been many reports of potent ALK inhibitors discovered by innovative pharmaceutical companies.Methods: A series of 2,4-diarylaminopyrimidine-containing ALK inhibitors were synthesized by Kim as the data set for the 3D-QSAR studies are described in this paper. CoMFA and CoMSIA models were performed using Sybyl X 2.0 package. Molecular docking analysis was carried out using Surflex-Dock in the SYBYL-X 2.0 package. Results: Firstly, The detailed contour analysis of ligand-based CoMFA and CoMSIA models enabled us to identify several structural requirements as mentioned in above paragraph for the observed inhibitory activities: 1) R1: bulk substituents, electronegative substitutes at para-site of R1 aromatic ring, electropositive substitutes at 2-site and 5-site of R1 aromatic ring, hydrophobic, and hydrogen bond acceptor (favorable); 2) R2: small substitutes, hydrophobic and H-bond donor (favorable); electrostatic field had little effect on biological activity; 3) R3: medium sized substitutes and electronegative substituents at orth-site of R3 aromatic group, H-bond donor at 2-site and 3-site of R3 aromatic group, and hydrogen bond acceptor at the para-site of R3 aromatic group (favorable); small substitutes and electrostatic field at para-site of R3 ring, and hydrophobic had little effect on biological activity. Scondly, the conformations obtained after MD is more stable than the docked conformations. MD simulation is performed in a more realistic environment, and much closer to physiological conditions. Conclusion: The contour maps obtained from the CoMFA, CoMSIA analysis provided useful information about the intermolecular interactions of the inhibitors with the surrounding environment. In addition, the 3D-QSAR models, molecular docking and MD simulations exhibit a good consistency indicating that the derived models are reliable and robus. The results from the 3D-QSAR models, molecular docking, and MD simulations should lead to a better understanding of the structural features needed to create novel potential ALK inhibitors.