Slope failures lead to catastrophic consequences in numerous countries, so accurate slope stability evaluation is critical in geological disaster prevention and control. In this study, the type and characteristics of slope protection structure disease were determined through the field investigation of an expansive soil area, and this information is incorporated into the numerical simulations and works to develop prediction models of slope stability. Four base machine learning (ML) methods are used to capture the relationship between protection structure diseases and factor of safety (FOS). Further, with the help of stacked generalization (SG), four ML models are combined, and the final SG model is used to predict the FOS. The results show that ML methods can effectively utilize this information and achieve excellent prediction results. The proposed SG model exhibits superior accuracy and robustness in predicting FOS compared to other ML methods. With FOS as the regression variable, the main feature contributions are slope height (37.05%) > slip distance of retaining wall (25.43%) > expansive force (18.03%) > slope gradient (12.00%); the coupling relationship among features is also captured by the proposed model. It is concluded that the SG method is particularly suitable for slope stability modeling under small sample conditions. Besides, the SG-based model effectively captures the impact of protection structure diseases on slope stability, enhances the interpretability of the ML model, and provides a reference for the maintenance and repair of the protection structure.