Tarim River Basin (TRB) is one of ecological environment vulnerable areas. Due to the matching of material and energy existed in some problems, the different fragility characteristics occurred obviously. According to related principles of ecological environment quality assessment, combined with ecological environment situation of Tarim River Basin, 20 indexes were selected, and the indicator system for synthetically ecological environment assessment was built. Moreover, ecological fragility index was set up, which can be used to indicate the degree of ecological environment quality in Tarim River Basin. The results were as follows: Aksu River Basin belongs to improved area. Yerkart River Basin and the upper reaches of TRB belongs to balance areas and Hetian River Basin and the middle reaches of TRB belongs to maladjustment areas. The lower reaches of TRB belongs to severe damage area. The assessment results are consonant with actual situation, which play an important function in ecological environment construction.