The invention relates to the field of laser cutting motion control of metal tubes, in particular to a method for determining the position of a mechanical center of a rotating shaft of a metal tube cutting system. In the method for determining the position of the mechanical center of the rotating shaft of the metal tube cutting system, a capacitive height adjustment device is used. The method is characterized by comprising the following specific steps: measuring the width W and the height H of a metal tube by using a caliper; then observing whether a sensing head of the capacitive height adjustment device is above the metal tube or not; if the sensing head of the capacitive height adjustment device is not above the metal tube, adjusting the position of a cutting nozzle; carrying out rough flattening operation; carrying out rough centering operation; carrying out accurate flattening operation; and carrying out accurate centering operation. By the rough flattening operation, the circumstance that the height adjustment device collides with the tube accidently due to excessive inclination of the tube is avoided; by the rough centering operation, the approximate position of the center of the tube is calculated, and the height adjustment device is prevented from pricking the outside of the square tube; after rough flattening and rough centering are carried out, flattening precision is improved by the accurate flattening operation, and flattening is finished; and finally, by the accurate centering operation, high-precision measurement on the mechanical center is finished.