In the context of high-quality development, scientifically and objectively assessing regional ecosystem health (EH) is important for ecological civilization. However, the commonly used EH assessment framework typically neglects intrinsic connections, mutual adaptability, and coordination among interrelated indicators. The coupling coordination model was utilized to improve the classic pressure–state–response assessment (PSR) model. The carbon footprint, water footprint, landscape pattern, and response status of the Manas River Basin were used to construct a medium-scale regional EH assessment framework linking natural ecosystems with human socioeconomic elements. A quantitative assessment was conducted on the EH conditions of the Manas River Basin from 2000 to 2020. Over the past 21 years, the EH conditions of the Manas River Basin have fluctuated upward. The ecosystem health index (EHI) increased from 0.18 to 0.37. Compared with the conventional PSR model, the coupling coordination pressure–state–response model (CC–PSR) better reflected the fluctuations in EH conditions caused by “pressure”, “state”, and “response” level changes. In the early stage (2000–2006), increasing human activity strongly pressured the regional ecosystem, limiting EH improvements. The increase in “pressure” was reflected in the increasing trends of the water footprint, carbon footprint, and ecological footprint. During the middle to late period (2009–2020), as the “response” level improved, the regional EH condition continued to increase, and the EHI stabilized between 0.29 and 0.38. Ecosystem resilience improvements and human afforestation projects enhanced the “response” level, but their impacts were noticeably delayed. Over the past 21 years, regional landscape diversity, landscape connectance, and landscape contagion have remained high. The well-maintained landscape pattern has laid the foundation for consolidating and improving the regional EH. The EHI is increasing; its fluctuations stem from periodic fluctuations in the regional water yield and carbon sequestration capacity, which are constrained by the basin climate and vegetation coverage. This study provides a scientific model for basin EH assessment.