Abstract: The manned lunar research station is an important basic facility for achieving medium- and long-term deep lunar exploration, and at the same time is a system project with multiple complex challenges. In this paper, from an architectural perspective, design constraints at macro, meso, and micro levels were analyzed first, and an implementation method for the architectural design of the manned lunar research station was provided using systems engineering, which consisted of four dimensions: the overall goal is “safety, sustainability, and intelligence”; the application ideas included process integration, model visualization, and design modularity; the application advantages are high efficiency, accuracy, and integration; the application framework was divided into application layer, model layer, and data layer. Finally, a three-dimensional structural model of architectural design system engineering was constructed, which included time dimension, logic dimension and knowledge dimension, and comprehensively embodied the structure of each task and related scientific knowledge in each stage, aiming to provide new perspectives and new ideas for the construction of manned lunar research station.