Accelerated urbanization has changed land use patterns, leading to the deterioration of ecosystems. Assessments of ecosystem health (ESH) during the urbanization process are used to determine the reasons and mechanism for this, and to uncover negative factors. In this study, we assessed the ESH of Qiannan prefecture, in Guizhou Province, China, based on the ecosystem services value. We selected a series of indicators, including natural, social, and economic aspects, to detect the impact of urbanization on ecosystem services in 1990, 1995, 2000, 2005, 2010, and 2015. The results show that ESH in Qiannan declined from 1990 to 2015, especially in the eastern and northern regions. Further, the results indicate that urbanization had a negative impact on ESH, of which the dominant factor was the proportion of construction land from 1990 to 2005. After 2005, moreover, the dominant factor was the gross domestic product. The impact of urbanization on EHS had spatial differences, however. The most significant negative impact was found in the east and north. After 2010, the western and central regions of Qiannan showed an urbanization trend in favor of ecosystem health. We recommend ecological restoration in regions with weak and relatively weak ESH levels to achieve sustainable development.