The invention discloses a rotary low-temperature hydrogen isotope separation system and a separation method thereof, which solve the complicated construction, complicated parameter control, and high operation cost, or helium gas supply requirement, hydrogen and helium separation, and complex separation column regeneration treatment, or high cost of palladium displacement chromatogram filling material and easy failure in the prior art. The separation system includes a cryogenic tank, a reversing frame, a separation column, a raw material hydrogen-storage tank, a light isotope storage tank, a heavy isotope storage tank, a vacuum pump, and an exhaust gas storage tank. The separation method is characterized in that a separation column absorbing the raw material hydrogen to gradually separate the liquid nitrogen liquid level to desorb the hydrogen isotope to complete rearrangement of hydrogen isotope in other separation columns; and the light and heavy isotopes can be finally collected respectively from the far and near ends of the loop. The system creatively utilizes the technical principle of a simulated moving bed, the hydrogen isotope can continuously circulate in the closed loop separation loop, the heavy isotope concentration gradually decreases from the near end to the far end where the desorption occurs in the separation loop, and the concentration gradient of the heavy isotope is continuously increased with the adsorption / desorption frequency.