The present invention relates to the preparation process of carbon nanotube with mixed isotope. The preparation process includes the following steps: setting one carbon rod including at least two different carbon isotope segments in set thickness as anode, with the different isotope segments in the rod length direction being able to be combined arbitrarily; setting one cathode set corresponding to the carbon rod; and arc discharge between the anode and the cathode for different carbon isotope segments the carbon rod provides to react in preset order to generate carbon nanotubes with different mixed isotopes and deposited on the cathode.