This study aimed to investigate and quantify the relationship between climate variation and incidence of Vibrio parahaemolyticus in Taiwan. Specifically, seasonal autoregressive integrated moving average (ARIMA) models (including autoregression, seasonality, and a lag-time effect) were employed to predict the role of climatic factors (including temperature, rainfall, relative humidity, ocean temperature and ocean salinity) on the incidence of V. parahaemolyticus in Taiwan between 2000 and 2011. The results indicated that average temperature (+), ocean temperature (+), ocean salinity of 6 months ago (+), maximum daily rainfall (current (−) and one month ago (−)), and average relative humidity (current and 9 months ago (−)) had significant impacts on the incidence of V. parahaemolyticus. Our findings offer a novel view of the quantitative relationship between climate change and food poisoning by V. parahaemolyticus in Taiwan. An early warning system based on climate change information for the disease control management is required in future.