Accurate and efficient acquisition of soil water and salt information is a prerequisite for the improvement and sustainable utilization of saline lands. With the ground field hyperspectral reflectance and the measured soil water-salt content as data sources, we used the fractional order differentiation (FOD) technique to process hyperspectral data (with a step length of 0.25). The optimal FOD order was explored at the correlation level of spectral data and soil water-salt information. We constructed two-dimensional spectral index, support vector machine regression (SVR) and geographically weighted regression (GWR). The inverse model of soil water-salt content was finally evaluated. The results showed that FOD technique could reduce the hyperspectral noise and explore the potential spectral information to a certain extent, improve the correlation between spectrum and characteristics, with the highest correlation coefficients of 0.98, 1.35 and 0.33. The combination of characteristic bands screened by FOD and two-dimensional spectral index were more sensitive to characteristics than one-dimensional bands, with the optimal responses of order 1.5, 1.0 and 0.75. The optimal combinations of bands for maximum absolute correction coefficient of SMC were 570, 1000, 1010, 1020, 1330 and 2140 nm, pH were 550, 1000, 1380 and 2180 nm, and salt content were 600, 990, 1600 and 1710 nm, respectively. Compared with the original spectral reflectance, the validation coefficients of determination (Rp2) of the optimal order estimation models for SMC, pH, and salinity were improved by 1.87, 0.94 and 0.56, respectively. The overall GWR accuracy in the proposed model was better than SVR, where the GWR optimal order estimation models Rp2 were 0.866, 0.904 and 0.647, and the relative per-centage difference were 3.54, 4.25 and 1.86, respectively. The overall spatial distribution of soil water and salt content in the study area was characterized by low in the west and high in the east, with more serious soil alkalinization problems in the northwest and less severe in the northeast. The results would provide scientific basis for the hyperspectral inversion of soil water and salt in the Yellow River Irrigation Area and a new strategy for the implementation and management of precision agriculture in saline soil areas.