The invention provides biocompatible carbon nanotube polymer and a preparation method thereof. The preparation method comprises the following steps: mixing and ball milling carbon nanotubes and potassium hydroxide, adding water for dissolving and ultrasound treating, and filtering and drying to obtain surface-hydroxylated carbon nanotubes; stirring and dissolving 2-dodecylsulfanylthiocarbonylsulfanyl-2-methylpropionic acid, dicyclohexylcarbodiimide, 4-dimethylaminopyridine and dichloromethane; subjecting the surface-hydroxylated carbon nanotubes and dichloromethane to ultrasound treatment; mixing above mixed liquid, and filtering and drying to obtain solid A; stirring and reacting 2-methacryloyloxyethyl phosphorylcholine, butyl methacrylate, azoisobutyronitrile and absolute ethyl alcohol to obtain reaction liquid B; subjecting the solid A and absolute ethyl alcohol to ultrasound treatment, adding reaction liquid B and stirring, adding trichloromethane and ethyl ether and precipitating and filtering, and drying to obtain a final product. Biocompatibility of material can be effectively improved, reactions such as protein adsorption and blood coagulation are avoided, and the use in the biosensor field and biofuel cell field is facilitated.