In the process of virtual screening, various results of virtual screening base on various virtual screening strategies and methods. The rational methods must be got by experiment, it can instruct large scale virtual screening. The assay method of acetylcholinest-erase( AChE) inhibitors was introduced in this paper. More than four thousand compounds were detected by this method, and 34 compounds with higher bioactivities were found. Based on two complex crystal structures, two virtual screening model were established to forecast the possible activity compounds from the compounds detected by applying 6 different methods. The two set possible activity compounds of the two model and the common possible activity compounds were compared with the activity compounds obtained from bio-assay. The important factors of virtual screening acetylcholinesterase (AChE) inhibitors and the methods to enrich activity compounds were analyzed and discussed. Some advices for large scale virtual screening of acetylcholinesterase( AChE) inhibitors were put forward.