Getting an objective, scientific and general ecosystem health assessment is the precondition and foundation of watershed management. This paper reviewed the concept and content of the NWA assessment system (natural constraint factor-watershed health indicator factor-anthropogenic disturbance factor" assessment system), and selected twelve indicators and constructed the model based on the character of Jinchuanhe River Basin. The assessment result showed that the ecosystem health threshold was distributed between 1.48 and 7.98, and the overall situation was worse. Scores were basically a ladder descending from the runoff area of the upper reaches to the dissipation area of the middle reaches and then to the runoff lost area of the lower reaches. As, This paper includes a comparative analysis among townships that are typical representatives of mountain, mountain-oasis, oasis, oasis-desert, desert area separately and found that their ecosystem health were gradually deteriorated.