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An iterative polynomial fitting method is proposed for the estimate of the baseline of the X-ray fluorescence spectrum signal. The new method generates automatic thresholds by comparing the X-ray fluorescence spectrum signal with the calculated signal from polynomial fitting in the iterative processes. The signal peaks are cut out consecutively in the iterative processes so the polynomial fitting will finally give a good estimation of the baseline. Simulated data and real data from the soil analysis spectrum are used to demonstrate the feasibility of the proposed method.