To deeply explore the characteristics of macrobenthos community in the lower reaches of the Dongwushi Reservoir of the Fuyang River, study the relationship between macrobenthos community and environmental factors, and comprehensively evaluate the water quality of the river, the composition and structural characteristics of macrobenthos community in the Fuyang River (Handan section) before flood season, during flood season, and after flood season were studied. Combined with the biological index (BI) and comprehensive water quality index, the water quality of the Fuyang River was analyzed, and the relationship between macrobenthos and physical and chemical factors of the water body was discussed by redundancy analysis; the main environmental factors affecting the characteristics of the macrobenthos community in the Fuyang River (Handan section) were determined. The results show that the average abundance of macrobenthos (26.3 ind./m²) before flood season is higher than that during flood season (13.5 ind./m²) and after flood season (14.1 ind./m²), and the change in the river’s water quantity during flood season has little influence on the structure of the biological community. Through comparative analysis, biotic index has an obvious effect on the biological evaluation and classification of water quality in the Fuyang River, and the water quality in the main city section is obviously worse than that in other sections. Before and after the flood season, dissolved oxygen (DO) and pH have significant effects on the community structure and distribution of macrobenthos in the Fuyang River, and water temperature and CODMn have significant effects during the flood season.