With the advancement of complex electronic equipment toward multi-functionality and high integration, the manufacturing of such equipment is trending toward smaller batches and greater variety. Existing manufacturing system models struggle to meet the demands for efficient production and rapid delivery. To address the increasing complexity of manufacturing and enhance the flexibility and adaptability of systems, this paper proposes the application of matrix-based manufacturing systems to the production of complex electronic equipment. This approach aims to improve the system’s ability to cope with dynamic changes. By analyzing the structure and variables of the system using system dynamics, a dynamic model is constructed. Subsequently, simulation and quantitative analysis are conducted to understand the interrelationships between internal variables, revealing their patterns of change, thereby achieving effective control over the complex electronic equipment manufacturing system.