Information security can ensure an efficient application of classified computers. At present, in some classified computers, there exist problems and deficiencies in the field of information security management. It is not conducive to the control of information security. A network parallel computing system is a network-based system that has a high potential to resolve these issues. In recent years, with the development of cost-effective CPU and high-speed network technology, this system has gradually attracted the attention of people. Based on the research on distributed parallel computing, this paper abstractly analyzes the network parallel computing environment. It also discusses how a security protection system solution based on a distributed enterprise network environment helps rectify this problem. After research and analysis of classified computer information systems, this paper uses distributed parallel computing for building an advanced security system. Experimental results show that this method can improve the security status of the system to a much higher extent compared to the existing network security technologies. It has strong practicality and good social and economic value. The purpose of this paper is to provide information management tools for enterprises to improve the secrecy of management-level enterprises.