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Effective pretreatment of spectral reflectance is vital to model accuracy in soil parameter estimation. However, the classic integer derivative has some disadvantages, including spectral information loss and the introduction of high-frequency noise. In this paper, the fractional order derivative algorithm was applied to the pretreatment and partial least squares regression (PLSR) was used to assess the clay content of desert soils. Overall, 103 soil samples were collected from the Ebinur Lake basin in the Xinjiang Uighur Autonomous Region of China, and used as data sets for calibration and validation. Following laboratory measurements of spectral reflectance and clay content, the raw spectral reflectance and absorbance data were treated using the fractional derivative order from the 0.0 to the 2.0 order (order interval: 0.2). The ratio of performance to deviation (RPD), determinant coefficients of calibration (R-c(2)), root mean square errors of calibration (RMSEC), determinant coefficients of prediction (R-p(2)), and root mean square errors of prediction (RMSEP) were applied to assess the performance of predicting models. The results showed that models built on the fractional derivative order performed better than when using the classic integer derivative. Comparison of the predictive effects of 22 models for estimating clay content, calibrated by PLSR, showed that those models based on the fractional derivative 1.8 order of spectral reflectance (R-c(2) = 0.907, RMSEC = 0.425%, Rp(2) = 0.916, RMSEP = 0.364%, and RPD = 2.484 >= 2.000) and absorbance (R-c(2) = 0.888, RMSEC = 0.446%, R-p(2)= 0.918, RMSEP = 0.383% and RPD = 2.511 >= 2.000) were most effective. Furthermore, they performed well in quantitative estimations of the clay content of soils in the study area.