To investigate the changes of water level and the distribution of snails in Anhui province before and after runs of the Three Gorges Reservoir Project, and to determine the relationship between the two factors and schistosomiasis transmission. The hydrologic data of Datong hydrologic station and the data of snail status and schistosomiasis morbidity in Anhui Province were collected. The data from 1991 to 2002 and 2003 to 2012 were considered as before and after the impoundment of the Three Gorges Reservoir Project. Based on the prevalence of schistosomiasis, the cases of people and cattle were speculated, and the average infection rate of people and cattle were calculated. The t-test was used to compare the difference of snail area and the density of living snails before and after the impoundment of the Three Gorges Project. The pearson method was used to analyze the relationship between water level and snail area. The spearman method was used to analyze the relationship between the water level and the distribution of snails. From 1991 to 2012, the range of the highest water level, the lowest water level, the difference between the highest and lowest water level, the mean in the abundant water seasons, the mean in the dry water seasons, and the difference between the abundant water seasons and the dry water seasons was 11.40-16.30, 3.68-5.20, 6.70-12.12, 9.92-14.40, 4.77-7.64 and 4.13-8.93 m, respectively. The snail areas was (28 613 ± 362) hm² and (29 477 ± 918) hm² (t = -3.00, P = 0.007), the density of living snails was 1.51 (1.15-2.43) and 0.43 (0.29-1.10) snails/0.11 m² (H = 4.28, P < 0.001) before and after the impoundment of the Three Gorges Project, respectively. The average infection rate of people and cattle was 1.68% (99 482/5 935 147) and 4.62% (13 923/3 011 33), and the average number of acute schistosomiasis cases was 328, before the impoundment of the Three Gorges Project; 0.60% (39 747/6 649 380), 1.65% (1 291/783 224) and 71 after the impoundment of the Three Gorges Reservoir Project, respectively. The snail areas had negative correlation with the highest water level, the difference between the highest and lowest water level, the mean in the abundant water seasons (r value was -0.514, -0.509 and -0.477; P value was 0.014, 0.015 and 0.025, respectively). The infection rate of people had positive correlation with the highest water level, the difference between the highest and lowest water level, the mean in the abundant water seasons (r value was 0.532, 0.587 and 0.446; P value was 0.011, 0.004 and 0.038, respectively). The infection rate of cattle had positive correlation with the highest water level, the difference between the highest and lowest water level (r value was 0.507 and 0.553; P value was 0.016 and 0.008, respectively). The number of acute schistosomiasis cases had positive correlation with the highest water level, the difference between the highest and lowest water level (r value was 0.481 and 0.486; P value was 0.023 and 0.022, respectively). Following the runs of the Three Gorges Reservoir Project, the change of water level in the section of Anhui Province affected the distribution of snails and the infection of people and cattle to some extent. The snail areas showed an upward trend, and the density of living snails, the infection rate of people and cattle showed a downward trend. The runs of Three Gorges Reservoir Project has certain role to reduce flood and helpful for schistosomiasis control.