The design and production of prefabricated buildings pose challenges in achieving standardization, limiting their extensive adoption. In order to address issues of prefabricated components, such as the low reusability of design knowledge, limited standardization, and design disconnection, this paper adopted the prefabricated cantilevered structure components as the research object. It employs knowledge-based engineering (KBE) theory and secondary split modularization approach in conjunction with Revit secondary development technology to establish a modular design system. The system formalizes complex design knowledge into concise user interfaces and a logically clear programming language, ensuring the design system’s ease of use and accessibility. To validate the authenticity and applicability of the modular design system developed in this paper, a comparison is made between the traditional modeling tool and modular modeling tool. Through empirical analysis, the result indicates that the new tool proposed in this paper can enhance the efficiency of design professionals by 72.92%. Among these, the tool meets the modeling and design requirements of 96.1% of the prefabricated components in the project, making it highly suitable for the modeling and design process of the vast majority of prefabricated components. Therefore, this design approach, which integrates KBE and three-dimensional geometric technology, makes the modular design of prefabricated cantilevered structural components feasible, providing a reference for future research in the design of other prefabricated components.