The computer numerically controlled (CNC) system is the key functional component of CNC machine tool control systems, and the servo drive system is an important part of CNC systems. The complex working environment will lead to frequent failure of servo drive systems. Taking effective health management measures is the key to ensure the normal operation of CNC machine tools. In this paper, the comprehensive effect of fault prediction and fault diagnosis is considered for the first time, and a health management system for machine tool servo drive systems is proposed and applied to operation and maintenance management. According to the data collected by the system and related indicators, the technology can predict the state trend of equipment operation, identify the hidden fault characteristics in the data, and further diagnose the fault types. A health management system mainly includes fault prediction and fault diagnosis. The core of fault prediction is the gated recurrent unit (GRU). The attention mechanism is introduced into a GRU neural network, which can solve the long-term dependence problem and improve the model performance. At the same time, the Nadam optimizer is used to update the model parameters, which improves the convergence speed and generalization ability of the model and makes it suitable for solving the prediction problem of large-scale data. The core of fault diagnosis is the self-organizing mapping (SOM) neural network, which performs cluster analysis on data with different characteristics, to realize fault diagnosis. In addition, feature standardization and principal component analysis (PCA) are introduced to balance the influence of different feature scales, enhance the feature of fault data, and achieve data dimensionality reduction. Compared with the other two algorithms and their improved versions, the superiority of the health management system with high-dimensional data and the enhancement effect of fault identification are verified. The relative relationship between fault prediction and diagnosis is further revealed, and the adjustment idea of the production plan is provided for decision makers. The rationality and effectiveness of the system in practical application are verified by a series of tests of fault data sets.