Natural indigo is a traditional dye for textiles. However, a large number of impurities on the surface of dyed fibers have been reported, which leads to poor friction and electrical performance, and exerts a negative impact on the spinning of the fibers. In this paper, a centrifugation pretreatment of the leuco indigo dye liquid was reported to remove the impurities, and the centrifuged dye was then applied to cotton fiber. The results revealed that centrifugation could effectively remove 88.2% of solid impurities, and the fiber after being dyed showed a clean and smooth surface. There was almost no chromatic aberration compared with the original fibers that were dyed with the noncentrifuged dye solution, and the optimized value of the color difference was less than 0.5. The friction and electrical properties of the fibers were improved. There was significantly reduced dust observed during the spinning process of the dyed fibers, and the spinnability of the fibers was improved. The coefficient of variation of single yarn decreased from 28.35% to 21.19%.