As the core components of high-precision rotary machine tools, machine tool bearings are prone to failure or damage, and their running state directly affects the safety and reliability of the entire equipment. Therefore, the paper proposes an intelligent operation and health management method for machine tool bearings based on Bayes-VMD-KPCA, Bayes-CNN-SVM, and health status evaluation index. Aiming at the complex working environment and high nonlinear degree of fault features of machine tool bearings, the Bayes-VMD-KPCA algorithm is used to perform variational mode decomposition of the original signal of the bearing fault, which avoids the influence of background noise and solves the problem of high dimension of multi-domain fault feature set. Second, the CNN-SVM fault diagnosis model uses a convolutional neural network (CNN) to deeply mine the extracted multi-domain fault features, and a support vector machine (SVM) can be used as a fault classifier to complete the diagnosis of various fault types of machine tool bearings. At the same time, the Bayes algorithm is introduced to tune the hyperparameters in the CNN-SVM model to further improve the prediction performance of the CNC machine tool-bearing fault diagnosis model. The results show that the intelligent operation and maintenance and health management method of CNC machine tool bearings proposed in this paper can effectively complete the fault type diagnosis and health status assessment of bearings, and its accuracy index reaches 99.33%. Compared with the single SVM model, Bayes-CNN model, Bayes-SVM model, and CNN-SVM model, the health effect is evaluated. The accuracy is increased by 6.33%, 4.33%, 2.66%, and 1%, respectively. It can be seen that the proposed method can more effectively realize the monitoring and health management of bearing fault.