Vibrio parahaemolyticus is a bacterial pathogen commonly detected in fishery products. However, incidences of this pathogen in fishery products reported in previous studies varied dramatically. This study aimed at producing reliable estimates of prevalence and geographical distribution of Vibrio parahaemolyticus in fishery products in China, by the use of hierarchical random effects Bayesian modelling. Results indicated that national incidence of Vibrio parahaemolyticus in fishery products in China was 15.66% (95% CI, 12.88%–18.80%), and remained steady during the period of 2008–2017. Incidences of Vibrio parahaemolyticus in fishery products were generally higher in Southeast compared with the remaining part of China, and varied among different categories of fishery products as well as in different seasons of year. The methods described in this study generated reliable information on the incidence of Vibrio parahaemolyticus associated with fishery products and their geographical distributions in China, and could be used by regulatory authorities and other researchers to quantify prevalence of other food safety hazards associated with specific foods in a given market.