The invention discloses an interactive visual aided drug design system and an implementing method. The design system comprises a molecule drawing module, a molecule format conversion module, a molecule display module, an operation module, a file parsing module, a communication module, a molecule similarity screening module, a client activation module, a server user management module and a setting module. The operation module mainly comprises a user defined compound library and a web database which is provided by the system. The server user management module comprises a user request processing module, a certificate generation module, a mailing module and a verification module. According to the arrangement, molecules drawn by the user or existed molecules or ligands acquired from a PDB (protein data bank) are served as the screening input molecules, the screening mode is selected by the user to perform corresponding screenings, and finally, according to ranks, the screening result is displayed through the analysis file.