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Toxic metals have attracted great concern worldwide due to their toxicity and slow decomposition. Although metal concentrations can be accurately obtained with chemical methods, it is difficult to map metal distributions on a large scale due to their inherently low efficiency and high cost. Moreover, chemical analysis methods easily lead to secondary contamination. To address these issues, 110 topsoil samples were collected using a soil sampler, and positions for each sample were surveyed using a global navigation satellite system (GNSS) receiver from a coal mine in northern China. Then, the metal contents were surveyed in a laboratory via a portable X-ray fluorescence spectroscopy (XRF) device, and GaoFen-5 (GF-5) satellite hyperspectral images were used to retrieve the spectra of the soil samples. Furthermore, a Savitzky–Golay (SG) filter and continuous wavelet transform (CWT) were selected to smooth and enhance the soil reflectance. Competitive adaptive reweighted sampling (CARS) and Boruta algorithms were utilized to identify the feature bands. The optimum two-stage method, consisting of the random forest (RF) and ordinary kriging (OK) methods, was used to infer the metal concentrations. The following outcomes were achieved. Firstly, both zinc (Zn) (68.07 mg/kg) and nickel (Ni) (26.61 mg/kg) surpassed the regional background value (Zn: 48.60 mg/kg, Ni: 19.5 mg/kg). Secondly, the optimum model of RF, combined with the OK (RFOK) method, with a relatively higher coefficient of determination (R2) (R2 = 0.60 for Zn, R2 = 0.30 for Ni), a lower root-mean-square error (RMSE) (RMSE = 12.45 mg/kg for Zn, RMSE = 3.97 mg/kg for Ni), and a lower mean absolute error (MAE) (MAE = 9.47 mg/kg for Zn, MAE = 3.31mg/kg for Ni), outperformed the other four models, including the RF, OK, inverse distance weighted (IDW) method, and the optimum model of RF combined with IDW (RFIDW) method in estimating soil Zn and Ni contents, respectively. Thirdly, the distribution of soil Zn and Ni concentrations obtained from the best-predicted method and the GF-5 satellite hyperspectral images was in line with the actual conditions. This scheme proves that satellite hyperspectral images can be used to directly estimate metal distributions, and the present study provides a scientific base for mapping heavy metal spatial distribution on a relatively large scale.