This study aimed to examine the association between floods and the morbidity of acute hemorrhagic conjunctivitis (AHC) in Mengshan, China. Relying on the longitudinal data, a generalized additive model (GAM) was applied to quantify the relationship between the morbidity of AHC and floods from 2005 to 2012, controlling for other meteorological variables. Years lived with disability (YLDs) and attributable YLDs were used as the measure of the burden of AHC because of the floods. Multivariable analysis showed that floods were significantly associated with an increased risk of the morbidity of AHC (rate ratio [RR] = 2.136, 95% CI: 2.109-2.163). The total YLDs per 1,000 in Mengshan was 0.2001, although the value in females was higher than that in males (0.2351 versus 0.1686). The YLD per 1,000 of AHC in Mengshan was highest between the ages of 5 and 14 years (0.6530), followed by the age of 0-4 years (0.3325). The attributable YLD per 1,000 of AHC due to the floods in Mengshan was 0.0434 (95% CI: 0.0425-0.0442). Our study confirms that floods have significantly increased the risks of AHC in the selected study area. Females and youngsters may be the vulnerable populations to develop the flood-related disease.