The invention discloses a method for removing amorphous carbon in carbon nanotubes, which comprises the following steps: suspending the carbon nanotubes into molten salt solution, and introducing oxygen or air into the molten salt solution. The oxidation reaction of the amorphous carbon and oxygen in the oxygen or the air is performed to generate carbon dioxide at a temperature of between 400 and600 DEG C, while the oxidation reaction of the carbon nanotubes of crystal structures is almost not performed at the temperature. Because a molten salt solution system has uniform temperature withoutthe phenomenon of local overheating, the carbon nanotubes are prevented from being oxidized because of local high temperature. Simultaneously, because the nanotubes are in the molten salt solution all the time, the carbon nanotubes are not easy to bring out from access environment by air flow so as to reduce the loss of the carbon nanotubes and avoid environmental pollution. After a period of time, the amorphous carbon is oxidized and removed; the molten salt solution blocks after being cooled; molten salt blocks are taken out and put into pure water to dissolve molten salt completely to obtain the carbon nanotubes of which the amorphous carbon is removed through filtration or centrifugal sedimentation.