The complex application software system is the systematic project characterized by the interdisciplinary integration, large amount of data interaction, frequent state change and high difficulty in the technology development. Its configuration management is one of the important factors to determine success or failure. The ‘localization’ transformation of the critical configuration management is carried out by analyzing challenges and requirements of the technical management for the simulation system of the ship’s overall performance. New ideas and suggestions are also proposed for the practical configuration management, which are preliminarily applied during the system development. It can provide reference for the development of the complex application software system under the mass innovation mechanism.