The computation time consuming and poor efficiency of prediction exist in the model selection of traditional SVM. By studing on kernel matrix, a SVM-based prediction method for selecting the optimal model framework SVR-D1.2 was proposed with the help of the kernel matrix’s symmetry and positive definition and kernel alignment. The method was applied to the prediction of wheat scab, and comparison experiments were done with the main existing methods. The result shows the method has more efficiency and precision of prediction in the occurrence tendency of wheat scab. Meanwhile, it is simple, practicable.