Peak ground acceleration (PGA) prediction is of great significance in the seismic design of engineering structures. Machine learning is a new method to predict PGA and does have some advantages. To establish explainable prediction models of PGA, 3104 sets of uphole and downhole seismic records collected by the KiK-net in Japan were used. The feature combinations that make the models perform best were selected through feature selection. The peak bedrock acceleration (PBA), the predominant frequency (FP), the depth of the soil when the shear wave velocity reaches 800 m/s (D800), and the bedrock shear wave velocity (Bedrock Vs) were used as inputs to predict the PGA. The XGBoost (eXtreme Gradient Boosting), random forest, and decision tree models were established, and the prediction results were compared with the numerical simulation results The influence between the input features and the model prediction results were analyzed with the SHAP (SHapley Additive exPlanations) value. The results show that the R2 of the training dataset and testing dataset reach up to 0.945 and 0.915, respectively. On different site classifications and different PGA intervals, the prediction results of the XGBoost model are better than the random forest model and the decision tree model. Even if a non-integrated algorithm (decision tree model) is used, its prediction effect is better than the numerical simulation methods. The SHAP values of the three machine learning models have the same distribution and densities, and the influence of each feature on the prediction results is consistent with the existing empirical data, which shows the rationality of the machine learning models and provides reliable support for the prediction results.