Abstract: Urban-rural spatial patterns and their economic-social systems have significantly transformed in the context of the rapid global urbanization and industrialization. However, the spatial governance practices are also constrained after these shifts. The urban-rural separation has also generated systemic discontinuities in the infrastructure allocation, public service provision, and social governance. The development structure further induces the inequities in the resources underpinning well-being. There is also the multidimensional interplay of the ecological environment, socio-economic circumstances, and differentiated urban-rural conditions. Urban areas are typically concentrated in the wealth of public services; Conversely, the rural base areas benefit from the ecological advantages and strong social capital, but suffer from the limited services accessibility and economic opportunities. Moreover, the extensive peri-urban and interface zones are characterized by semi-urbanization and ambiguous spatial identities. Conventional governance categories frequently fell outside to impede the coherent functional articulation between urban and rural systems. It is often required for urban-rural integration. Particularly, the urban and rural spaces can constitute a continuous gradient with the multiple levels, nodes, and transitional forms, rather than a rigid binary. In this study, an alternative analytical lens was used to capture the dynamic reconfiguration of the urban-rural relations and spatial function. Crucially, there was the complex and multi-dimensional interaction between the urban-rural continuum and human well-being. The spatial pattern was interdependent among ecosystems, economic activities, social structures, and individual perceptions. The urban-rural continuum was characterized by the continuity of the space and the gradation of the functions. Human well-being included the objective dimensions within this framework, such as the material living standards, health, educational, ecological integrity, and subjective dimensions on the perceived quality of life. A systematic coupling was also linked with the space, the factor flow, and public services from a system perspective. There was a relationship between the urban-rural continuum and human well-being, rather than the conventional urban-rural dichotomy. The continuum approach was selected for the urban-rural space as an integrated gradient, differentiated transitional zones (highly urbanized, moderately developed, and conventional agricultural types), and base areas. A more detailed identification of the spatial heterogeneity and functional complementarities was obtained to detect the disparities in human well-being along the gradient. Nonetheless, this framework alone was insufficient for the governance challenges from the blurred boundary and intensified factor circulation. Adaptive governance was offered as a process-oriented paradigm under complex systems, with emphasis on iterative learning, dynamic adjustment, multi-actor collaboration, and resilience. The urban-rural continuum framework clarified the structural and relational mechanisms of the urban-rural interactions, while the adaptive governance provided the operational tools for the flexible intervention under uncertainty. A full-cycle regulation was proposed with the “pre-monitoring–mid-term regulation–post-feedback”. Adaptive governance strategies were tailored to the specific zones to coordinate the spatial optimization, factor mobility, and public service equalization. Ultimately, this finding can refine the urban-rural continuum and adaptive governance strategies for the heterogeneity after integration. This finding can provide the theoretical support and policy implications to promote urban-rural integration and sustainable agriculture.