The scientific assessment of the health level of county ecosystems is the basis for formulating county-based sustainable development strategies. In this paper, we take the county areas of Sichuan Province as the evaluation objects and combine the SDGs (the Sustainable Development Goals) to establish a county ecosystem health evaluation index system based on the VORS (Vigor–Organization–Resilience–Service) model. On this basis, we used the entropy weight method, the Moran index method, and the obstacle degree model to analyze the ecosystem health level, spatial distribution characteristics, and obstacles of 183 counties in Sichuan Province. The main results were as follows: (1) A total of 80.87% of the counties in Sichuan Province were at sub-healthy and healthy levels, concentrated in the southeastern part of Sichuan, and 19.13% of the counties were at an unhealthy level, mainly in the Aba, Ganzi, and Liangshan areas. (2) The health levels of county ecosystems in Sichuan Province had high spatial autocorrelation characteristics. The H–H (High–High) agglomeration area and the L–L (Low–Low) agglomeration area had significant agglomeration characteristics, which were distributed in the Cheng-Mian area and the northwestern Sichuan area, respectively. (3) The key indicators restricting the healthy development of urban ecosystems in Sichuan counties are economic vitality, economic resilience, and quality of life, all of which belong to the economic subsystems, with obstacles reaching 17.25%, 16.68%, and 13.52%, respectively. This study can provide theoretical and methodological support for research into ecosystem health evaluations at the county level, and provide a decision-making basis for promoting the health of county ecosystems and coordinating regional development in Sichuan Province.