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Measuring the soil salinity using visible and near-infrared (vis–NIR) reflectance spectra is considered a fast and cost-effective method. For monitoring purposes, estimating soils with low salinity measured as electrical conductivity (EC) using vis–NIR spectra is still understudied. In this research, 399 legacy soil samples from six regions of Southern Xinjiang, China with low EC values were used. Reflectance spectra were measured in the laboratory on dried and ground soil samples using a portable vis–NIR spectrometer. By using 10-fold cross-validation, three algorithms–partial least-squares regression (PLSR), random forest (RF), and <span style="font-variant: small-caps;">Cubist</span>–were employed to develop statistical models of EC. The model performance evaluation was obtained by the relative importance of variants. In terms of accuracy assessment of soil EC prediction, the results demonstrated that the <span style="font-variant: small-caps;">Cubist</span> model performed better (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mi>R</mi><mn>2</mn></msup></semantics></math></inline-formula> = 0.67, RMSE = 0.16 mS/cm, RPIQ = 2.28) than both PLSR and RF. Despite similar variants for modelling, the RF model performed somewhat better than that of the PLSR. Additionally, the 610 nm and 790 nm wavelengths only demonstrated significant promise for predicting low soil EC values when used in the <span style="font-variant: small-caps;">Cubist</span> mode. The current research recommends the use of <span style="font-variant: small-caps;">Cubist</span> to estimate the low soil salinity using the vis–NIR reflectance spectra.