To optimize the probe structure in time domain reflectometry (TDR) and establish a water / hydrate saturation measurement model based on TDR response, a numerical simulation model of TDR measurement process was established by using the finite element numerical simulation method. The numerical model was verified by using air as the measured medium first. Then the sodium chloride solution of different concentration and quartz sand with different hydrate saturation were used as the measured media, and the influence of the conductivity and dielectric constant of the measured medium on the reflection waveform was studied. The quartz sand with different water / hydrate saturation was simulated by changing the dielectric constant of the measured medium. It has been shown by the numerical data that the apparent dielectric constant decreases with the increase of hydrate saturation in quartz sand, thus propagation speed of electromagnetic wave increases in a nonlinear form, and the maximum error of the propagation speed obtained is within 5% compared with the theoretical values. Filling the tested area with anisotropic materials in the numerical model to simulate the hydrate-bearing sediment more realistically will be the future work.