The assessment of watershed ecosystem health promotes the construction of ecological civilisation in China, and assessment results are an important basis for watershed planning and management. At present, research on and application of small watershed ecosystem health assessment in China are deficient. Thus, small watershed protection and management in China are restricted. The research object of this study is a small watershed of Changqing River in Yongtai County of Fuzhou City. Using satellite image data, digital elevation data as well as field and monitoring data combined with 3S technology, the health status of the small watershed ecosystem was evaluated by three assessment systems consisting of remote sensing data, measured survey data and multi-source data. The watershed ecosystem health status was quantitatively analysed, and a comparative analysis with the results of different evaluation methods was conducted. Results show that, in general, the comprehensive indexes of ecosystem health obtained by the three evaluation methods are 70.29, 77.68 and 63.87. The evaluation results support the notion that the research status of the watershed ecosystem is satisfactory. The overall ecosystem health status of the high mountains sub-watershed in the northwest and in the southwest of the watershed is relatively acceptable but that of the middle and lower reaches is relatively poor. Finally, the evaluation results of the three methods were compared, and their differences were analysed, it can provide a basic idea for the ecosystem health evaluation of the small watershed.