Resonance is commonly used for in situ measurement of the dynamic elastic modulus to evaluate the strength of concrete samples. Many researchers are also exploring the application of this convenient measurement technology for safety monitoring. Nevertheless, the presence of cracks and variations in curing conditions within samples can impact the resonance frequency range, potentially leading to potential inaccuracies in measurements. In order to improve the measurement accuracy of resonance frequency, this study introduces the Generalized S-Transform (GST) algorithm for measuring the dynamic elastic modulus, which utilizes its high time-frequency resolution to scan the power peak-point in non-stationary and transient excitation signals to determine the resonance frequency. For concrete materials with lower consistency, the experimental results verify the high accuracy of this algorithm in measuring resonance frequency compared with Fast Fourier Transform (FFT). This provides a reference for using the algorithm to measure the dynamic elastic modulus in civil engineering applications, such as buildings and bridges.