The configuration management of civil aircraft brake control system plays a key role in the process of system design and development and airworthiness compliance verification. In order to improve the configuration management capability of civil aircraft brake system, the software designed and developed can meet the airworthiness requirements, this paper introduces the concept and method of brake system control software configuration management, and illustrates how to combine configuration management with software design by means of system thinking and information flow to carry out whole-life-cycle configuration management. By combining with the requirements of DO-178C, configuration data digital management mechanism based on product configuration is established, unique data source of brake control system development is created. The result shows that a unified configuration database is established with configuration baseline management combination in which the information and status are accurately recorded strictly to ensure the real-time, traceability, integrity and effectiveness of status information, and achieve the final configuration control goal to meet the airworthiness requirements.