The degradation of the ecosystem and the loss of natural capital have seriously threatened the sustainable development of human society and economy. Currently, most research on Gross Ecosystem Product (GEP) is based on statistical modeling methods, which face challenges such as high modeling difficulty, high costs, and inaccurate quantitative methods. However, machine learning models are characterized by high efficiency, fewer parameters, and higher accuracy. Despite these advantages, their application in GEP research is not widespread, particularly in the area of combined machine learning models. This paper includes both a GEP combination model and an explanatory analysis model. This paper is the first to propose a combined GEP prediction model called Ada-XGBoost-CatBoost (Ada-XG-CatBoost), which integrates the Extreme Gradient Boosting (XGBoost), Categorical Boosting (CatBoost) algorithms, and SHapley Additive exPlanations (SHAP) model. This approach overcomes the limitations of single-model evaluations and aims to address the current issues of inaccurate and incomplete GEP assessments. It provides new guidance and methods for enhancing the value of ecosystem services and achieving regional sustainable development. Based on the actual ecological data of a national city, data preprocessing and feature correlation analysis are carried out using XGBoost and CatBoost algorithms, AdaGrad optimization algorithm, and the Bayesian hyperparameter optimization method. By selecting the 11 factors that predominantly influence GEP, training the model using these selected feature datasets, and optimizing the Bayesian parameters, the error gradient is then updated to adjust the weights, achieving a combination model that minimizes errors. This approach reduces the risk of overfitting in individual models and enhances the predictive accuracy and interpretability of the model. The results indicate that the mean squared error (MSE) of the Ada-XG-CatBoost model is reduced by 65% and 70% compared to the XGBoost and CatBoost, respectively. Additionally, the mean absolute error (MAE) is reduced by 4.1% and 42.6%, respectively. Overall, the Ada-XG-CatBoost combination model has a more accurate and stable predictive performance, providing a more accurate, efficient, and reliable reference for the sustainable development of the ecological industry.