The invention relates to a method for preparing a functionalized carbon nanotube based on a polyethyleneimine, comprising the following steps of: (1) dipping the carbon nanotube in a strong acid for 2-4 hours, subsequently filtering, drying and storing the carbon nanotube; (2) conducting the circumfluence operation in the DMF of SOCl2 and introducing acyl chloride on the surface of the carbon nanotube and subsequently centrifuging and washing the carbon nanotube by the DMF; (3) dispersing the carbon nanotube in the DMF solvent and adding the DMF solution with PEI dissolved wherein; mixing the mixed solution by strong magnetic force; subsequently adding tri-ethylamine in the solution; repeatedly conducting a plurality of pure water dialysis after reaction; subsequently obtaining the CNT/PEI by freezing and drying; and (4) conducting acetylation reaction on the amino functional group on the surface of the CNI/PEI; or conducting carboxyl reaction on the amido on the surface of the CNT/PEI. The method has simple preparation process, moderate reaction condition, easy operation and industrial executive prospect; and the carbon nanotube prepared by the method can be dispersed in the solution for long, the agglomeration phenomenon does not occur and the carbon nanotube has excellent biocompatibility and safety in bio-medicals.