The present invention relates to a carbon nanotube transistor biosensor with aptamers and a method for detecting a target material using the same, more particularly to a carbon nanotube transistor biosensor recognizing the target material, i.e., a specific molecule (such as a protein, a peptide, an amino acid, and an organic/inorganic compound) by using DNA aptamers and a method for screening a target material using the same. In the biosensor of the present invention, the aptamers binding specifically to a particular protein are adsorbed on a carbon nanotube constituting the channel domain of carbon nanotube transistor to easily detect/identify a particular protein via the electric conductivity of carbon nanotube that varies if the particular protein is exposed to corresponding aptamers.