Rural ecosystem health (REH) serves as an effective metric for assessing the damage degree and stability state within rural systems and their components. It reflects the interaction and the balance among rural subsystems, emphasizing the harmonious development of resources, agriculture, environment, economy, and society that are fundamental to sustainable rural development. Most regional-scale ecosystem health assessments primarily focus on either the natural state of the ecosystem or external disturbances affecting it, often neglecting human ecological systems characterized by economic and social dimensions. Taking Chongqing as an example, we established an improved REH assessment framework by integrating ecological integrity from the perspective of a social-economy-natural compound ecosystem. Furthermore, we innovatively incorporated the Sustainable Development Goals (SDGs) into the formulation of the REH indicator system to quantitatively elucidate the spatiotemporal characteristics. The results indicated that: (1) The REH in Chongqing exhibited an evolutionary pattern characterized by a subsequent rise, maintaining values between 0.363–0.872 from 2000 to 2018. This trend reflected a distinct two-stage development characteristic, with the rural socio-economic subsystem contributing the most at 33.36%, followed closely by the rural environmental subsystem at 27.84%; (2) In 2018, the REH across the 36 districts and counties in Chongqing displayed spatial differentiation patterns described as “collapse in the west, high levels in the northeast, and localized surges”. The areas ranked from smallest to largest REH were metropolitan, western, southeastern, and northeastern areas; (3) Four levels (e.g., disease, single health, compound health, and comprehensive health) and twelve sub-levels of REH were defined using a dominant factors method. Finally, we analyzed the driving factors from four aspects of urbanization development: policy regulation, urban-rural factors flow, and regional differences. We also proposed differentiated planning and policies for sustainable rural development in Chongqing.