Abstract: Resonant ultrasound spectroscopy (RUS) allows identification of the elastic coefficients of solid materials vibrating under an ultrasonic excitation from the measurement of their inherent frequencies. Retrieving the resonant frequencies is therefore a key signal processing step in RUS. However, according to the attenuation characteristics of low Q-factor (quality factor) materials, the resonance spectrum obtained by the experiment is flat and the resonance frequencies can not be directly observed from the spectrum. Therefore, in order to retrieve more effective resonance frequencies than traditional approach from the low Q-factor materials, a new extraction method of resonance frequencies was proposed to solve the limitation in this paper. The empirical mode decomposition method was used to decompose the frequency response of the specimen into finite Intrinsic Mode Function (IMF) components with special oscillation characteristics. According to the prior information of resonant ultrasound spectroscopy (RUS),the relevant IMF component was selected to retrieve reliable resonance frequencies from the resonance spectrum. The short fiber filled epoxy (a kind of bone-like materials, Q \approx 25) was adopted as the specimen to calculate the elastic coefficients and engineering moduli compared with the traditional linear prediction method. The experimental results show that the new method has high computational efficiency and is more sensitive to the weak excitation modes of low Q-factor materials. The number of effective resonance frequencies (26) are more than traditional linear prediction methods (21), which also satisfied 5 times estimation requirement of elastic constants. In addition, the optimized elastic moduli are closer to the standard values of the short fiber filled epoxy. In conclusion, the EMD-based method can retrieve a sufficient quantity and effective resonance frequencies from the flat spectrum of low Q-factor materials, which can not only improve the reliability of the estimation of mechanical parameters, but also extend the application range of resonant ultrasound spectroscopy.