The business secret information is an important asset of an enterprise，and its safety is an important part of enterprise management. In 2010，the SASAC issued the “Interim Provisions on the protection of trade secrets of central enterprises”，and implemented the policy of standardizing in accordance with the law，enterprises being responsible，giving priority to prevention，highlighting priorities，facilitating work and ensuring safety. Taking the business secret protection of Kangyuan Pharmaceutical Co.，Ltd as a case，this paper analyzes the main points of protecting business secrets，and expounds the methods effects of system construction.