The association between floods and the risk of dysentery remain controversial. Therefore, we performed a meta-analysis to clarify this relationship. A literature search was performed in PubMed, Web of science, and Embase for relevant articles published up to November 2019. Random-effects model was used to pool relative risks with 95% confidence intervals. The sensitivity analysis was carried out to evaluate the stability of the results. Publication bias was estimated using Egger’s test. Eleven studies from 10 articles evaluated the association between floods and the risk of dysentery in China. The pooled RR (95% CI) of dysentery for the flooded time versus non-flooded period was 1.48 (95% CI: 1.14–1.91). Significant association was found in subgroup analysis stratified by dysentery styles [dysentery: 1.61 (95% CI: 1.34–1.93) and bacillary dysentery: 1.46 (95% CI: 1.06–2.01)]. The pooled RR (95%CI) of sensitivity analysis for dysentery was 1.26 (95% CI: 1.05–1.52). No significant publication bias was found in our meta-analysis. This meta-analysis confirms that floods have significantly increased the risk of dysentery in China. Our findings will provide more evidence to reduce negative health outcomes of floods in China.