For company operation which is a complex system with multi-inputs and multi-outputs, establishing a management information system is an inevitable choice. Starting from improving decision-making functions of Information system, taking data envelopment analysis as theoretical foundation, utilizing Visual Stutio, drawing support from C#, the article will design form-based application program based on the information management system DEA. What's more, through case studies, it illustrates the superiority of the DEA method in evaluating the efficiency of systems with multi-inputs and multi-outputs, as well as the usefulness in improving the decision support function of the enterprise information management system.