Accurate and timely monitoring of soil salinity is essential for the sustainable management and remediation of coastal salinization. This study utilized a UAV-based remote sensing platform to collect multispectral imagery and concurrent in situ soil salinity samples from an experimental zone within the Yellow River Delta National Nature Reserve in July 2024. We constructed multiple spectral indices and employed advanced feature selection methods—namely VIP, MultiSURF, and PSO-SFLA—to identify the most informative index combination. We established a soil salinity retrieval model utilizing a stacking ensemble framework. This architecture integrated TabPFN, SVM, and Ridge regression as the base learners, while employing XGBoost as the meta-learner to synthesize the final predictions. Model interpretability was assessed using SHAP (SHapley Additive explanations) values, while predictive performance was evaluated using the coefficient of determination (R²), Standardized Root Mean Square Error (S_RMSE), and the Ratio of Performance to Deviation (RPD). Results indicate that the stacking model, when coupled with PSO-SFLA for feature selection, outperformed all other model configurations. It achieved the highest prediction accuracy on the test set, with an R² of 0.754, S_RMSE of 0.310, and RPD of 1.941. The resulting soil salinity distribution map exhibited a high degree of spatial agreement with the ground-truth survey data. This study demonstrates that leveraging a stacking algorithm with UAV multispectral data provides an accurate and reliable method for monitoring soil salinity in coastal wetlands, offering valuable technical support for effective soil salinization management.