Abstract: Promoting the deep integration of the real and digital economies is crucial for building a modern industrial system during the 15th Five-Year Plan period. However, while digital technologies are becoming increasingly advanced, the actual integration benefits lag significantly behind. Existing literature predominantly relies on a “technology-led” perspective to emphasize the importance of integration, largely neglecting the crucial adaptive role of organizational forms as micro-institutional carriers. Drawing on organizational theory, the underlying mechanisms through which organizational forms empower the deep integration of the real and digital economies were systematically analyzed. The research indicates that internal restructuring towards flattening, end-to-end business process reengineering, cross-departmental coordination and incentives, coupled with the ecological complementarity of external industrial chains, can effectively reduce internal transaction costs and external collaboration barriers, thereby significantly enhancing integration efficiency and spillover effects. Current integration practices face four major structural barriers: corporate organizational transformation significantly lags behind digital deployment; the digital ecosystem in the manufacturing sector remains underdeveloped; there is a mismatch in market human capital; and constraints stem from the rapid iteration of intelligent agents alongside the inadequate supply of foundational software. To break through these bottlenecks, it is imperative to drive process reengineering through business-led initiatives, cultivate interdisciplinary talents with an application-oriented approach, and unleash the ecological vitality of various corporate entities. Doing so will fully release the powerful developmental momentum generated by digital innovation in traditional industries.