Southeast China is frequently hit by tropical cyclones (TCs) with significant economic and health burdens each year. However, there is a lack of understanding of what infectious diseases could be affected by tropical cyclones. This study aimed to examine the impacts of tropical cyclones on notifiable infectious diseases in southeast China. Disease data between 2005 and 2011 from four coastal provinces in southeast China, including Guangdong, Hainan, Zhejiang, and Fujian province, were collected. Numbers of cases of 14 infectious diseases were compared between risk periods and reference periods for each tropical cyclone. Risk ratios (RRs) were calculated to estimate the risks. TCs were more likely to increase the risk of bacillary dysentery, paratyphoid fever, dengue fever and acute hemorrhagic conjunctivitis (ps < 0.05) than to decrease the risk, more likely to decrease the risk of measles, mumps, varicella and vivax malaria (ps < 0.05) than to increase the risk. In conclusion, TCs have mixed effects on the risk of infectious diseases. TCs are more likely to increase the risk of intestinal and contact transmitted infectious diseases than to decrease the risk, and more likely to decrease the risk of respiratory infectious diseases than to increase the risk. Findings of this study would assist in developing public health strategies and interventions for the reduction of the adverse health impacts from tropical cyclones.