Determining and evaluating the key factors that effectively indicate river health status and its changes are critical for the eco-hydrological conservation of arid inland rivers and adaptive river management. Taking the Yarkant River mainstream as the research object, from the system theory point of view, 23 specific indicators were selected based on the conceptual model of "pressure-state-response" and the "achievable best state" reference standard to construct river health evaluation indicators and standards. The model of river health assessment based on the entropy of order is established to evaluate the river health of the Yarkant River in the arid region. The results showed that the current status of assessment of the target layer health level was 0.529, which was in the sub-health state (level III). The carded group of the river segment-Iganqi (S1) comprehensive health index (0.546) was better than the river section Yiqin-Erik Tamu (S2). The evaluation results are basically in line with the actual situation, and the health of the river is threatened, and it needs to arouse the attention of relevant departments.