Aim: To explore the binding mode of 2-substituted 1-indanone derivatives with acetylcholinesterase (ACHE) and provide hints for the future design of new de- rivatives with higher potency and specificity. Methods: The GOLD-docking con- formations of the compounds in the active site of the enzyme were used in subse- quent studies. The highly reliable and predictive three-dimensional quantitative structure-activity relationship (3D-QSAR) models were achieved by comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods. The predictive capabilities of the models were validated by an extal test set. Moreover, the stabilities of the 3D-QSAR models were veri- fied by the leave-4-out cross-validation method. Results: The CoMFA and CoMSIA models were constructed successfully with a good cross-validated coef- ficient (q2) and a non-cross-validated coefficient (r2). The q2 and r2 obtained from the leave-1-out cross validation method were 0.784 and 0.974 in the CoMFA model and 0.736 and 0.947 in the CoMSIA model, respectively. The coefficient isocontour maps obtained from these models were compatible with the geometrical and physi- cochemical properties of AChE. Conclusion: The contour map demonstrated that the binding affinity could be enhanced when the small protonated nitrogen moi- ety was replaced by a more hydrophobic and bulky group with a highly partial positive charge. The present study provides a better understanding of the inter- action between the inhibitors and ACHE, which is helpful for the discovery of new compounds with more potency and selective activity.