As one of the key ways to realize the industrialization and green development of construction, prefabricated construction is conducive to saving resources and energy and improving labor productivity and quality. Aiming to solve the problem of the lack of standardization in the design of prefabricated residential buildings, which leads to the components not being universally used and the industrial characteristics not being fully embodied, while excessive standardization leads to a lack of personalization and flexibility, the modular design theory is applied to the standardized design of prefabricated residential buildings in this study. The application route of modular design theory in the standardized design is constructed, that is, “system decomposition—module design—module combination”. Taking residential buildings within a height of 54 m as an example, each basic functional module is standardized and combined into standard plans. At the same time, the functional space module design based on modular coordination and the module combination design based on the trinity of “modulus, pattern, and mode” are discussed. This research is of great significance for giving full play to the comprehensive benefits of prefabricated concrete structures in quality improvement, cost reduction, and rapid assembly.