For a magnetically levitated flexible rotor (MLFR), the amount of residual imbalance not only generates undesired vibrations, but also results in excessive bending, which may cause it hit to the auxiliary bearings. Thus, balancing below the critical speed is essential for the MLFR to prevent the impact. This paper proposes a balancing method of high precision and high efficiency, basing on virtual trial-weights. First, to reduce the computed error of rotor's mode shapes, a synchronous notch filter is inserted into the active magnetic bearing (AMB) controller, achieving a free support status. Then, AMBs provide the rotor with the synchronous electromagnetic forces (SEFs) to simulate the trial-weights. The SEFs with the initial angles varying from 0 deg to 360 deg in the rotational frame system result in continuous changes in the MLFR's deflection. Last, correction masses are calculated according to the changes. Compared to the trail-weights method, the new method needs not test-runs, which improves the balancing efficiency. Compared to the no trail-weights method, the new method does not require a precise model of the rotor-bearing system, which is difficult to acquire in the real system. Experiment results show that the novel method can reduce the residual imbalance effectively and accurately.