Aiming at the defense situation of security and secrecy in the secret-involved information system, research the methods of anti-virus and anti-Trojan. Introduce the current principle and key technology of anti-virus and anti-Trojan software in the secret-involved information system, analyze the shortage of anti-virus and anti-Trojan software. Introduce a self-defined anti-virus and anti-Trojan assistant software, prevent the virus and Trojan through deploying dimensionalities anti-virus and anti-Trojan system, anti-virus scanning technology in the entrance of secret-involved information system and other assistant instrument to enhance security and secrecy. The result proves, the armament industry shall combine the anti-virus and anti-Trojan technology and security and secrecy works, manage normalization to affirm the safety and credibility of secret-involved information system.