In the prediction model for the maximum wind speed of typhoon,the number of the input variables is very large,so the situation of missing data is easy to happen.However,regression analysis cant deal with this situation.The paper proposes a method to predict missing data based on probabilistic principal component analysis (PPCA),which treats the abnormal data and the predictive variables as missing variables,and it takes Mahalanobis distance to reflect the exact relationship among process variables.The experimental result shows that this method is more flexible than the regression analysis,and it is more accurate.