Elastic properties of soft tissues are important indicators for disease progression. Previous studies have utilized mechanical resonance spectroscopy to infer elastic properties of soft tissues by extracting their resonance frequencies. However, the method to accurately obtain the elastic modulus from the resonance frequencies remains inconclusive. In this study, we report a method based on a multi-degree-of-freedom (MDOF) model to determine the Young's modulus of soft tissue samples from the measured resonance spectroscopy. Resonance frequencies of agar tissue phantoms with different elastic properties were obtained, and Young's modulus was calculated using the MDOF-based method. The result was validated by mechanical compression tests and finite element method simulations. The results show that the multi-degree-of-freedom (MDOF)-based method is capable of determining Young's modulus of soft tissue samples with various elasticities and dimensions. This study provides an opportunity to accurately assess the elastic properties of small-sized soft tissue samples.