The invention discloses a method for adjusting dynamic balance of a rotor of a magnetic suspension vacuum molecular pump, which particularly comprises fist, detecting an actual vibrating signal of a rotor which is obtained by a sensor directly from a rotor of a magnetic bearing, second, collecting rotor speed and phase signal, third, doing an isolating process of direct current composition to the vibrating signal of the rotor which is obtained, fourth, doing a real-time filtering process to the vibrating signal according to the rotor speed, obtaining vibrating signals with the same frequency of the rotor, fifth, finishing corresponding dynamic balance algorism in post period by utilizing a dynamic balancing device or an observation system which is operated in a magnetic suspension vacuum molecular pump, and doing a dynamic balance to the rotor according to the result of the dynamic balance algorism, sixth, repeating the steps untill the rotor achieves a needed dynamic balancing accuracy. The method of the invention has the advantages of high accuracy of a vibrating value which is collected, high dynamic balance accuracy, and balancing behavior of the rotor is completely consistent with the final actual operating behavior, which is beneficial for simplifying dynamic balancing equipment.