Based on information on ecology and socio-economics over the Tarim River Basin from 2000, we analyzed factors influencing ecosystem health, using index system method and expert score sheet, developed index weighting scheme of ecosystem health assessment, and evaluated ecosystem health in this basin. We found that the ecosystems in the mountainous areas of Aksu, Yarkant and kaidu-Konqi River Basin were sub-healthy, those in the Hetian River Basin was healthy; ecosystems in plain-oasis areas of Aksu, Yarkant and Hetian River Basin were healthy, those of Kaidu-Konqi River Basin were sub-healthy; the desert ecosystems of four headstreams were unhealthy; the ecosystems of the upper reaches of Tarim River were healthy, those of the middle reaches were sub-healthy, and those of the lower reaches were unhealthy. Evaluation results are consistent with the actual situation, indicating that our method is suitable for ecosystem health assessment in the Tarim River Basin. The resulting data provide scientific basis for integrative ecosystem management of the Tarim River Basin.