The flexible satellite batch production line is a complex discrete production system with multiple cross-disciplinary fields and mixed serial parallel tasks. As the source of the satellite batch production line process, the warehousing system has urgent needs such as uncertain production scale and rapid iteration and optimization of business processes. Therefore, the requirements and architecture of complex discrete warehousing systems such as flexible satellite batch production lines are studied. The physical system of intelligent equipment is abstracted as a digital model to form the underlying module, and a digital fusion framework of “business domain + middleware platform + intelligent equipment information model” is constructed. The granularity of microservice splitting is calculated based on the dynamic correlation relationship between user access instances and database table structures. The general warehousing functions of the platform are divided to achieve module customization, addition, and configuration. An open discrete warehousing system based on microservices is designed. Software architecture and design develop complex discrete warehousing systems based on the SpringCloud framework. This architecture achieves the decoupling of business logic and physical hardware, enhances the maintainability and scalability of the system, and greatly improves the system’s adaptability to different complex discrete warehousing business scenarios.