Abstract: Soil salinization has posed a serious threat to the growth and yield of crops in the national food security. Among them, the Taolai River basin with the widely distributed saline-alkali land has been one of the most important planting areas in northwest China. It is a high demand for the timely acquisition of soil salinity information during the salinization control. In this study, a representative sampling area of soil salinization was taken as the Bianwan Farm in Suzhou District, Jiuquan City, Gansu Province, China. A rapid inversion model of soil salinity was proposed at the soil depths of 0-15, 15-30, and 30-50 cm under the crop cover of alfalfa and corn in the phenological period. The multi-spectral image data of the Unmanned Aerial Vehicle (UAV) was also collected at the same time. The reflectance of the spectral band was extracted in the different acquisition points of plots. The red edge band was also introduced to calculate the spectral index, in order to effectively improve the inversion accuracy. A total of 58 spectral indices were involved in the modeling. The Support Vector Machine-Recursive Feature Elimination (SVM-RFE) was selected to screen the spectral index. Specifically, the SVM was used to sort the feature variables, and then evaluate the importance of each feature variable. The variables with low importance were removed, according to the backward iteration. As such, a better performance was achieved to effectively remove the redundant features for the high running speed of the model. A total of 36 models were constructed to evaluate the accuracy and inversion effect of the models, including Random Forest (RF), Extreme learning machine (ELM), and Back-propagation neural network (BPNN). The model input was taken as the unfiltered full and filtered new variable group. Finally, the best soil-salinity inversion model was determined for the optimal inversion depth under crop coverage. The results show that the SVM-RFE variable selection significantly improved the accuracy of each soil-salinity inversion model. A better performance was achieved in the coefficient of determination (R2), root-mean-square error (RMSE), and training speed of the improved model, compared with the model without variable screening. Overall, the inversion effect of the RF model was better than that of ELM and BPNN models. Among them, the inversion effect was one of the best indicators for real soil salt. Specifically, the RF model presented the best inversion effect in the 0-15 and 30-50 cm soil layers under crop cover, where the Rp2 values of the validation set in the alfalfa field were 0.71 and 0.58, respectively, RMSEp values were 0.026 and 0.033, respectively; the Rp2 values in the corn field were 0.67 and 0.64, respectively, the RMSEp values were 0.111 and 0.094, respectively. In the 15-30 cm layer, the ELM model presented the best inversion effect, where the Rp2 values in the alfalfa and corn fields were 0.58, and 0.039, respectively; the RMSEp values were 0.68, and 0.059, respectively. In the terms of inversion depth, the inversion effects of 0-15 cm and 30-50 cm were better than that of 15-30 cm for the alfalfa-covered soil. The inversion effects of 0-15 cm and 15-30 cm were better than that of 30-50 cm for the corn-covered soil. The comprehensive analysis showed that the 0-15 cm soil layer was the best inversion depth for the soil salt content under crop cover, where the average R2 of the validation set was 0.65, and the RMSE was 0.084. A strong reference was offered to manage the saline-alkali land in the arid area of northwest China. The finding can also provide a scientific basis for the rapid inversion of salt in the different soil depth layers under crop mulching.