Over the past five decades, the Research Center for Eco-Environmental Sciences of the Chinese Academy of Sciences (CAS) and its predecessor and associated laboratories -including the Key Laboratory of Systems Ecology of CAS (established in 1986), the State Key Laboratory of Urban and Regional Ecology (established in 2006), and the recently approved State Key Laboratory of Regional and Urban Ecology (2025) -have made seminal contributions to the development and application of the social-economic-natural complex ecosystem (SENCE) theory. Initially proposed in 1984 by Shijun Ma and Rusong Wang, SENCE theory is an interdisciplinary, holistic, and integrative framework for understanding the complex interactions and feedback mechanisms between social, economic, and natural subsystems. SENCE theory has underpinned the development of the pattern-process-service-sustainability (PPSS) research paradigm, which has been used to systematically analyze the dynamics of fragile ecosystems such as the Loess Plateau and to design innovative solutions for ecological restoration and sustainable regional development. The theory has also significantly advanced research in ecosystem services and ecological security, providing the scientific basis for key national initiatives such as ecological function zoning, the ecological conservation redline policy, and the establishment of China's national park system. Furthermore, the development and application of SENCE theory have catalyzed the emergence of urban ecology as a distinct interdisciplinary field in China, exemplified by the establishment of the country's first urban ecosystem research station in Beijing. This station has generated long-term ecological data on, novel theoretical insights into, and practical policy support for sustainable urban planning and management. In addition, grounded in SENCE theory, a series of pioneering sustainability models have been developed and implemented, including China's first "ecological province " (Hainan), "ecological city " (Yangzhou), "ecological county " (Dafeng), and the first national pilot program for realizing the value of ecological products (Lishui). These models have shown how the SENCE approach can effectively bridge ecological conservation and socio-economic development, providing practical pathways for regional sustainability. Looking ahead, SENCE research will continue to advance theoretical understanding, enhance computational modeling and simulation capabilities, and strengthen evidence-based policy-making. By aligning with China's national ecological civilization strategy as well as global sustainability agendas, future research within this framework will not only inform the construction of a "Beautiful China " but also contribute Chinese wisdom and solutions to global ecological governance.