Two-Way Satellite Time and Frequency Transfer based on Software Defined Receiver (SDR-TWSTFT) link collects the measurement data per second, and then the original data is fitted into a set of observation files of 300 seconds by mathematical model. Therefore, the time transmission result of the link is affected by short-term measurement noise and non-modeled error, showing a certain characteristic of random noise. In this paper, a frequency domain amplitude analysis method is proposed to determine the filter factor and construct a low-pass Vondrak filter. Through the analysis of SDR-TWSTFT link measurement data between National Time Service Center (NTSC) of Chinese Academy of Sciences and Physikalisch Technische Bundesanstalt (PTB) of Germany, it is found that this method is effective for filtering the high frequency noise within one day of the average time, and can improve the reliability of the SDR-TWSTFT link time transfer results. At the same time, the short-term frequency and time stability of the link after filtering are also significantly improved.