An effective method was proposed to remove obstinate boron nitride phase impurities in boron nitride nanotubes (BNNTs). The method is based on strong interactions between BNNTs and a conjugated polymer wrapping them and significant weight and size difference between BNNTs and impurities. The as-grown samples and purified samples were compared through detailed characterization, using scanning electron microscopy, transmission electron microscopy, and Raman and Fourier transformed infrared spectroscopy. The results reveal that impurities are effectively removed and resultant BNNTs possess perfect crystallization.