To eliminate the electric feed-through introduced into the measurement of the micro-resonator by the electrical scheme, an improved mixed-frequency-excitation (MFE) method is proposed in this paper. Based on the electromechanical coupling and electric feed-through model of the micro-hemispherical resonator (MHR), the mechanism of suppressing the effect of electric feed-through on the resonant signal by the MFE method of different harmonic signals is analyzed theoretically. The MFE method can be divided into two kinds according to the frequency range. The feasibility of the method is verified by the actual measurement, and the multiplexing of the same oscillator can realize the MFE for the resonator. The measured results show that the resonant response of the micro-resonator can be measured by scanning frequency, and the signal-to-noise ratio can reach more than 10dBV. The resonant frequency of the resonator can be determined according to the position of the resonant peak. The characteristics and application range of the MFE methods of two different harmonic signals are deeply analyzed. It is revealed that the reason why the MFE in the high-frequency range causes the resonance peak deviation is due to the electrostatic negative stiffness introduced by the electric feed-through. The method and research content presented in this paper have a certain application prospect in the measurement of micro-capacitive resonators.