Objective This study aimed to assess the transmission risk of schistosomiasis along the middle and lower reaches of Yangtze River after flooding in 2020. Methods Snail survey and survey for contamination with wild feces in snail breeding environment were conducted in Hunan, Hubei, Jiangxi, Anhui, and Jiangsu Provinces in October, 2020. According to the historical epidemic of schistosomiasis and the flooding record, two counties of each province were selected for this study, including Nanxian, Huarong, Hanchuan, Yangxin, Lushan, Lianxi, Guichi, Zongyang, Luhe, and Hanjiang. Two townships (town) were selected from each county, and then one administrative village was selected from each township (town) for the survey. Using systematic sampling and environmental sampling method, snail survey was performed in two categories of environment in the current flood-affected area, including snail-infested environment bearing frequent human and animal activities in 2017—2019, and in environment of historically snail-free or snail-free over 20 years. All the collected snails were examined for schistosome infection by loop-mediated isothermal amplification (LAMP) method. During collecting snails from environments, wild feces were collected as well and tested by miracidia hatching method (one sample, triple detection). Chi-square test is used to compare the difference of occurrence rate of frames with living snails surveyed using systematic and environmental sampling methods. Results A total of 64 snail breeding environment sites were surveyed, from where 8 904 snails were collected, of them 7 918 were alive. The overall occurrence rate of living snail frames was 11.7% (1 813/15 464), and the rates were 10.5% (679/6 441) using environmental sampling method and 12.6% (1 134/9 023) using systematic sampling method. The difference between the two rates was statistically significantly (χ² = 14.91, P < 0.01). The occurrence rates of living snail frames by systematic sampling in Zongyang and Guichi of Anhui Province were 60.2% (607/1 008) and 28.4% (251/882), respectively, which were both significantly higher than the rates in other counties (P < 0.01). The average density of live snails in Zongyang (2.177/0.1 m²) and Guichi (3.323/0.1 m²) were over ten folds higher than those in other counties. One sample collected from in Guichi was found schistosome positive detected by LAMP method. A total of 100 wild feces samples were collected from 47 snail breeding environment, three of them were found schistosome positive, which belong to cattle, located in two environments in Lushan, Jiangxi and one environment in Guichi, Anhui. A total of 572 snails were collected from 44 sites of historically snail-free environment and the environment of snail-free for over 20 years, and 550 living snails were detected. These snails were found in the potential spreading areas in one environment in Guichi, Anhui, and two environments in Lushan, Jiangxi, with the average occurrence rates of living snail frames by systematic sampling being 21.2% and 4.5% respectively, showing the average densities of living snails being 1.254/0.1 m² and 0.081/0.1 m² respectively. Two samples collected from Lushan, Jiangxi were detected as schistosome positive by LAMP. Conclusion The flooding in 2020 may expand the schistosomiasis transmission areas in middle and lower reaches of Yangtze River, among them the transmission risk in Anhui and Jiangxi Provinces rose, compared to the previous year.