The rapid identification of foodborne pathogenic bacteria is an important task. Compared with the traditional detection methods, Raman spectroscopy is a non-destructive testing method and can simultaneously enhance the identification speed. In order to improve the accuracy and efficiency of Raman spectroscopic identification of Escherichia coil O157∶H7 and Brucella suis vaccine strain S2, a integral classification model is proposed based on the principal component analysis and the Stacking algorithm, whose robustness is improved by the grid search and K-fold cross validation. It is experimentally confirmed that compared with the logistic regression, K nearest neighbor, support vector machine and other single models, the integral model based on the Stacking algorithm possesses the highest accuracy rate of 99.73% the expected result is achieved.