A new method of modal balancing for flexible rotors considering the impact of elastic supports is proposed since flexible rotors supported on elastic supports cannot be efficiently balanced using the current modal balancing method. A finite element model of a rotor is established and a rotor test rig is built up. After calculating and measuring critical speeds and vibration modes, modal balancing is conducted through the rotor testing system. Results suggest that the relative error between the calculated and measured critical speeds is only 0.36% and the modal assurance criterion of the first calculated and measured mode shapes is 0.990 6. The method of modal balancing for flexible rotors considering elastic supports is reasonable, the algorithms are correct and the number of trial mass can be reduced under the premise of ensuring fully orthogonal balance. A combination of calculated support stiffness, i.e., an elastic support at left end and a rigid support at right end, is accordant with the actual situation of rotor structure and the vibration reduction percentages from CH1 to CH3 reach more than 80% and CH4 up to 38%. As the overall damping effect is obvious, the modal balancing method considering elastic supports has a prospect in engineering application and it can provide technical reference for balance tests of flexible rotors in aero engines.