Navy equipment software is safety critical software. Software safety is an important factor for naval equipment achieving combat mission successfully. According to characteristics of navy equipment system and its software, this paper has proposed a software safety engineering method basing on system theory. Further, it has described safety tasks in each stage included in software lifecycle. Finally, according to the goal of software safety, it has presented software safety management system to ensure safety of naval equipment software. The research has positive significance for healthy development of navy equipment software.