With the completion and use of BDS-3, this paper proposes two improved methods for retrieving tide surface height from global navigation satellite system reflectometry (GNSS-R) based on the BDS-3/GPS multi-frequency signal to noise ratio data, namely, method of eliminating gross errors based on the relationship between the highest peak and the second peak and the method of optimal frequency band. The effectiveness of the method is verified by the observation data of 333-337 consecutive 5 days of accumulated days (DOY) in 2020 at the MAYG station on Mayotte near the Indian Ocean. The results show that the method of removing gross errors based on the relationship between the highest peak and the second peak can improve the accuracy of tide level inversion. The GPS frequency band is increased by 9.16% and the BDS frequency band is increased by 17.34%, but it will reduce the number of inversion results. The optimal frequency band correction method can improve the accuracy while increasing the number of inversion results. The inversion accuracy of the corrected GPS S1C and S2W frequency bands is increased by 26.54% and 22.89%, respectively. In BDS S1X, S2I, S6I, and S7I, the 5-day tide level inversion root-mean-square error decreased by 61.36%, 34.23%, 47.68%, and 55.38% respectively. The accuracy improvement is higher than the former.