The multiphase components of natural ice contain gas, ice, unfrozen water, sediment and brine. X-ray computed tomography (CT) analysis of ice multiphase components has the advantage of high precision, non-destructiveness and visualization; however, it is limited by the segmentation thresholds. Due to the proximity of the CT value ranges of gas, ice, unfrozen water, sediment and brine within the samples, there is uncertainty in the artificial determination of the CT image segmentation thresholds, as well as unsuitability of the global threshold segmentation methods. In order to improve the accuracy of multi-threshold segmentation in CT images, a CT system was used to scan the Yellow River ice, the Wuliangsuhai lake ice and the Arctic sea ice. The threshold ranges of multiphase components within the ice were determined by watershed algorithm to construct a high-precision three-dimensional ice model. The results indicated that CT combined with watershed algorithm was an efficient and non-destructive method for obtaining microscopic information within ice, which accurately segmented the ice into multiphase components such as gas, ice, unfrozen water, sediment, and brine. The gas CT values of the Yellow River ice, the Wuliangsuhai lake ice and the Arctic sea ice ranged from −1024 Hu~−107 Hu, −1024 Hu~−103 Hu, and −1024 Hu~−160 Hu, respectively. The ice CT values of the Yellow River ice, the Wuliangsuhai lake ice and the Arctic sea ice ranged from −103 Hu~−50 Hu, −100 Hu~−38 Hu, −153 Hu~−51 Hu. The unfrozen water CT values of the Yellow River ice and the Wuliangsuhai lake ice ranged from −8 Hu~18 Hu, −8 Hu~13 Hu. The sediment CT values of the Yellow River ice and the Wuliangsuhai lake ice ranged from 20 Hu~3071 Hu, 20 Hu~3071 Hu, and the brine CT values of the Arctic sea ice ranged from −6 Hu~3071 Hu. The errors between the three-dimensional ice model divided by threshold ranges and measured sediment content were less than 0.003 g/cm3, which verified the high accuracy of the established microscopic model. It provided a scientific basis for ice engineering, ice remote sensing, and ice disaster prevention.