Soil salinization is an essential risk factor for agricultural development and food security, and obtaining regional soil salinity information more reliably remains a priority problem to be solved. To improve the accuracy of soil salinity inversion, this study focuses on the Manas River Basin oasis area, the largest oasis farming area in Xinjiang, as the study area and proposes a new soil salinity inversion model based on stacked integrated learning algorithms. Firstly, we selected four machine learning regression models, namely, random forest (RF), back propagation neural network, support vector regression, and convolutional neural network, for performance evaluation. Based on the model performance, we selected the more effective RF and BPNN as the basic regression models and further constructed a stacking integrated learning model. This stacking integration learning model improved the prediction accuracy by training a secondary model to fuse the prediction results of these two basic models as new features. We compared and analyzed the stacking integrated learning model with four single machine learning regression models. Findings indicated that the stacking integrated learning regression model fitted better and had good stability; on the test set, the stacking integrated learning regression model showed a relative increase of 8.2% in R2, a relative decrease of 14.0% in RMSE, and a relative increase of 6.5% in RPD when compared to the RF model, which was the single most effective machine learning regression model, and the stacking model was able to achieve soil salinity inversion more accurately. The soil salinity in the oasis areas of the Manas River Basin tended to decrease from north to south from 2016 to 2020 from a spatial point of view, and it was reduced in April from a temporal point of view. The percentage of pixels with a high soil salinity content of 2.75–2.80 g kg−1 in the study area had decreased by 19.6% in April 2020 compared to April 2016. The innovatively constructed stacking integrated learning regression model improved the accuracy of soil salinity estimation on the basis of the superior results obtained in the training of the single optimal machine learning regression model. As a consequence, this model can provide technological backup for fast monitoring and inversion of soil salinity as well as prevention and containment of salinization.
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