River ecosystem health assessments provide the foundation for river ecological protection and integrated management. To evaluate the aquatic ecosystem health of the Fan River basin, benthic macroinvertebrate indices (the Multimeric Macroinvertebrates Index Flanders (MMIF) and Family Biotic Index (FBI)), a habitat index (the river habitat quality Index (RHQI)) and a water quality index (the Improved Water Pollution Index (IWPI)) were selected. The entropy weighting method was used to calculate the RHQI and IWPI. A fuzzy comprehensive evaluation method was used to evaluate the aquatic ecosystem health. The evaluation results indicated that the aquatic ecosystem health of the Fan River basin was better in 2018 than in 2011, which respectively belonged to the ends of the 11th and 12th Five-Year Plans of the Major Science and Technology Programs for Water Pollution Control and Treatment in China. The proportions of sampling stations with good, moderate and poor grades in 2011 were 50.0%, 40.0% and 10.0%, respectively, and in 2018, the proportions of stations with excellent, good and moderate grades were 20.0%, 50.0% and 30.0%, respectively. A correlation analysis showed that the RHQI was significantly correlated with the MMIF, FBI and IWPI. The riparian land use pattern was an important factor that influenced changes in the aquatic ecosystem health grade. Of the water quality parameters, total phosphorous (TP) and potassium bichromate index (COD) were the main factors that affected the characteristics of benthic macroinvertebrates and the aquatic ecosystem health.