The invention discloses a nanotube-based fluorescence marked carrier and a preparation method thereof. The fluorescence marked carrier comprises a nanotube inner wall, a quantum structure and a nanotube outer wall. The size of the nanotube structure is designed according to the characteristics of a simulated carrying object, and the size of the nanotube structure is regulated and controlled accurately by controlling the growth condition; in the fixed-temperature annealing process, a nanowire in a core-shell structure is guaranteed to be decomposed completely and the quantum structure limited between the nanotube inner wall and the nanotube outer wall is not damaged; the fluorescence marked part of the nanotube adopts a semiconductor quantum structure, has high fluorescence intensity, long duration time and stable photochemical property, is insusceptible to photobleaching and realizes high-efficiency radiative recombination; furthermore, continuous broad spectrum excitation can be adopted, the absorption coefficient is big, fluorescence emission peak is narrow, wavelength trailing is avoided, and the distinguishing degree is high; the nanotube structure can realize fluorescence marked carrying of the carrying object in the tube and also can perform the traditional wrapping or combined type fluorescence marked carrying.