Under the accelerated transition toward greenization, intelligentization, and industrialization in the construction industry, and in response to the national trinity strategy integrating education, science and technology, and talent development, architectural universities are compelled to reform the cultivation system for top-notch innovative talents through deep integration of research and education. Grounded in the requirements of emerging engineering education and considering the practical and interdisciplinary nature of architectural disciplines, this paper systematically examines critical issues in the current talent development process, such as the disconnect between engineering practice and scientific research innovation capacity. The study proposes a core educational philosophy of “research-education integration rooted in engineering fundamentals,” defines the objectives for cultivating top-notch innovative talents, and constructs an integrated model encompassing four key dimensions: curriculum restructuring, faculty development, platform resource integration, and innovation capability enhancement. Implementation mechanisms such as task-driven pedagogy, seamless undergraduate-doctoral training, and project-team-platform synergy are also elaborated. The concepts and pathways explored in this study may offer theoretical foundations and practical insights for fostering top-notch innovative talents in architectural universities within the new engineering context.