Abstract: The five-element connection number (FECN) method is a systematic analysis method for the uncertain factors in the system by using the opposition, difference and identity of each factor to analyze the factors. In view of the advantages of the FECN, which could simultaneously consider the certainty and uncertainty factors in the river health evaluation, an index system of 24 indicators in five categories including the river’s natural morphology, water quality, sediment, aquatic organisms and ecological environment, and social services was established in the case of Shenyang Section of Liaohe Conservation Area. By using analytic hierarchy process to determine the weight, a comprehensive evaluation model of five-element relation number was constructed to evaluate the river health in Shenyang Section of Liaohe Conservation Area. The results showed that the FECN of river health evaluation in Shenyang Section of Liaohe Conservation Area was 0.576 8, and the river health grade was medium. Among them, the connection number of river natural morphology was 0.932 9, and the evaluation level was medium. The connection number of water quality was 0.550 4, and the evaluation level was unhealthy. The connection number of sediment condition was 0.920 9, and the evaluation level was excellent. The connection number of aquatic organisms and ecological environment was 0.781.3, and the evaluation level was good. The connection number of social services was 0.478 3, and the evaluation level was medium. The sediment heavy metal pollution in Shenyang Section of Liaohe Conservation Area was relatively light, but the riverbed stability was poor, the water nitrogen and phosphorus pollution were serious, and the fish diversity was not high. It is suggested that the treatment and management of the reserve should be further strengthened by strictly controlling the discharge of sewage, strengthening the management of water resources, improving the utilization rate of chemical fertilizer, and strengthening the restoration of riparian zone, etc.