The establishment and development of the Guangdong–Hong Kong–Macao Greater Bay Area have demonstrated the collaborative relationship of the globally regional reconstructing. As a major strategy of the Greater Bay Area, Northern Metropolis faces challenges in transboundary ecological collaborative management. Based on the analysis of the ecological issues and the complexity of the transboundary management in Shenzhen Bay, this article proposes a co-governed “Special Ecological Conservation Zone” under the context of “one country, two systems” by zoning areas with varied protection levels. The development and operation framework includes: establishing an independent Joint Work Group, building consensus and standardizing collaboration procedure, conducting hierarchical management and regulating development, leveraging and motivating knowledge and technological innovation, and strengthening community engagement and emphasizing shared benefits. By case-studying three sites along the Shenzhen Bay, this article also provides place-making strategies for different levels of protection zones. Exploring innovative collaboration models for Northern Metropolis, this article is expected to provide new solutions for the sustainable development of the Greater Bay Area and creative insights for global transboundary ecological collaborative management.