Due to the lack of strict periodicity in link noise of two-way satellite time and frequency transfer, when calculating the frequency drift of hydrogen atomic clocks through least squares fitting, some link noise will be included, resulting in bias in the calculation of link noise. Regarding this issue, the accurate frequency drift of the hydrogen atomic clock could be worked out by comparing the clock bias between the hydrogen and cesium clocks within the local timekeeping station. Furthermore, frequency drift of hydrogen clocks across different sites could be obtained. This method could reduce the impact of frequency drift on least squares fitting and obtain more accurate total noise data.The results indicate that this hydrogen-cesium joint two-way satellite time and frequency transfer noise correction method reduces the noise calculation deviation from 10ns to 0.3ns compared to the calculation method only relying on hydrogen atomic clocks, effectively improving the accuracy of link noise calculation.