The rising sea level caused by global climate change might impact the human living environment. Global navigation satellite systems (GNSS)-multipath reflection (MR) technology holds significant potential for monitoring tide level changes. GNSS-MR technology typically employs low-order polynomials to extract the signal-to-noise ratio (SNR) residuals containing GNSS interference signals. It utilizes Lomb-Scargle (LSP) spectral analysis or empirical mode decomposition (EMD) to obtain the dominant frequency of the SNR residuals, which is then converted into tidal heights. However, as the satellite elevation angle increases, the GNSS interference signals decrease and the traditional method does not adapt well to the extraction of SNR residuals under such conditions. A series of improved EMD-kind algorithms, namely ensemble empirical mode decomposition (EEMD), complementary ensemble empirical mode decomposition (CEEMD), complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN), and improved complete ensemble empirical mode decomposition with adaptive noise (ICEEDMAN), have been proposed to address the shortcomings of EMD algorithms such as end effect and mode aliasing. However, these improved EMD-kind algorithms have yet to be reported in sea level inversion. This study investigates the mitigation effects of EMD-kind algorithms on GNSS-MR direct signal and noise to improve the stability and accuracy of an SNR residual sequence with high satellite elevation angles. Experimental data from the HKQT station for one week and the SC02 station for one year are utilized to validate the effectiveness and accuracy of these algorithms in extracting SNR residuals. Compared to the traditional polynomial method, the experimental results demonstrate that all EMD-kind algorithms effectively address the distortion issue in traditional inversion methods under long periods, higher satellite elevation angles, and low GNSS receiver sampling rates. Among these algorithms, the results from the experiments show that ICEEMDAN consistently provides the best inversion accuracy. The results of the comparative analysis show that ICEEMDAN effectively reduces non-interference signals in SNR residuals at higher satellite elevation angles, expanding the useable range of satellite elevation angles and improving the utilization and temporal resolution of GNSS data inversion. Hence, it is an effective and appropriate approach to improving the accuracy of GNSS-MR tide level monitoring.