Abstract: In order to explore the macrobenthic community structure and its influencing factors in the main stream of the Manao River, water quality monitoring and macrobenthic sample collection were carried out in January 2021 (low-water period) and August 2021 (high-water period), and habitat conditions and environmental characteristics were investigated and recorded. The FBI and RDA were used to explore the main influencing factors of water environment and macrobenthic community structure in each period. The results show that: (1) There were significant spatial and temporal differences of the macrobenthic community structure in the main stream of the Manao River. A total of 691 macrobenthos were collected in high and low water periods, belonging to 2 phyla, 4 classes, 10 orders, 26 families, 28 species, and a total of 18 dominant species. The number of individuals, abundance, and the number of dominant species all showed a high-water period > low-water period, among which the species of Bivalvia were the most abundant in low-water period, and the species of Insecta were the most abundant in high-water period. (2) The water quality of the main stream of the Manao River in low-water period is mainly moderate and mild pollution, while the high-water period the water was mainly very clean and extremely clean. Water pollution was mainly concentrated in the upper and middle reaches of the river, and the water quality was improved compared with the previous year. (3) Water temperature (WT), flow rate (Vel) and phosphate (PO₄³⁻) were the main environmental factors affecting the community structure of macrobenthos in low-water periods, and COD_Mn in high-water periods. The results showed that there were significant differences in the community structure of macrobenthos and its main environmental factors in the main stream of The Manao River in different water cycles. The water quality was good in wet season, but there were pollution in some reaches of the river in dry season, which should be paid more attention to.