Traditional methods of flexible rotor balancing need to add trail weights and run the rotor many times, resulting in a low balancing efficiency and a poor security. To solve this problem, a modal balancing method for high speed flexible rotor without trail weights is proposed. Modal information is obtained by finite element software and vibration data are measured to calculate the size and orientation of the unbalance mass. In order to easily and comfortably apply this method to engineering practice, a balancing system corresponding to the proposed method is developed, including software and hardware. The phase measurement error between the system and similar foreign advanced testing equipment SIRIUS is 2.376. Further, the results of rotation speed calibration shows the measurement range of the system is 0～60kr/min with an error less than 10%. Finally, a two-disk flexible rotor across the second order critical speed is balanced using the system. After balancing, the amplitude of the rotor at the first order critical speed reduces by 60.6%, the amplitude at the second order critical speed reduces by 74%. The results demonstrate that the system can be effectively applied to perform flexible rotor balancing, improving the efficiency and safety of balancing.