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Optical remote sensing satellites provide rapid access to regional topsoil salinization mapping. However, mapping topsoil salinization based on spectral reflectance is always affected by background material like vegetation cover, straw mulching and soil types. In light of these challenges, this study investigates the potential of image fusion, where images of original and bare soil pixels were combined, to minimize the impact of vegetation cover on topsoil salinity mapping. A case study was presented for the typical vegetation cover area using synchronized Sentinel-2 MSI image (named original image) and 255 ground-truth data collected in October 2020, aligning with periods of vegetation cover and salt return. Furthermore, to obtain novel bare soil pixels, multi-temporal Sentinel-2 MSI images were acquired during two distinct intervals: March to May and September to November, spanning the years from 2018 to 2021. The synthetic soil image (SYSI) was obtained by extracting bare soil pixels from multi-temporal images. Two images (original, SYSI) were fused with non-negative matrix factorization (NMF) method, named SYSIfused. Then, the stacking machine algorithm was used for soil salinity mapping under different soil types, with evaluating the impact of SYSIfused on the accuracy of soil salinity prediction. The results showed the SYSIfused outperformed the original image (the R2 of the best models increased by 0.054–0.242, RMSE and MAE decreased by 0.049–0.780 and 0.012–0.546, respectively). Based on the SYSIfused, the order of the effect of soil types was coastal bog solonchaks > alluvial soil > cinnamon soil > coral saline soil > overall samples, and their roles in improving the R2 of the model were 0.141, 0.085, 0.022, 0.012, respectively. Besides, stacking models with the SYSIfused provided the best prediction performances (R2 = 0.742, RMSE = 0.377, MAE = 0.362). This study introduces the concept of merging original images with SYSI, resulting in a significant improvement in the accuracy of soil salinity mapping in areas covered by vegetation.