To explore the correlation between Vibrio parahaemolyticus (VP) contamination of aquatic products and clinical diarrhea cases. Methods Totally 654 aquatic product samples and 8 112 clinical diarrhea cases were collected in Huzhou City between 2014 to 2016. Aquatic products and faecal or anal swab specimens of clinical diarrhea cases were tested for VP, O group of serum and the virulence gens tdh and trh, respectively. The distribution characteristics of VP in aquatic products and clinical diarrhea cases was analyzed and compared. Results The detection rate of VP in aquatic products was 28.02% (183/653), of which freshwater products and seafood counted for 33.67% (132/392) and 19.54% (51/261) respectively, and the difference was statistically significant (χ²=14.823, P<0.001). The detection rate of VP in clinical diarrhea cases was 4.87% (395/8 112), and 15.40% (170/1 104) of them had exposure to aquatic and its products. In the time distribution, the detection rate of VP in aquatic products and clinical diarrhea cases were basically the same, and the detection rates were relatively high in July to September. In the serotype distribution, O3 and O4 were the two main serotypes both in aquatic products and clinical diarrhea cases. In the virulence genotype distribution, the tdh()/trh() was predominant (60.51%, 239/395) in clinical diarrhea cases, while the tdh()/trh() was the predominant one (42.08%, 77/183) in aquatic products. Conclusion There was a certain correlation between VP contamination in aquatic products and clinical diarrhea cases in the time distribution and biological characteristics. Therefore, it is necessary to further strengthen the monitoring and management of VP in aquatic products.