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In existing global navigation satellite system-interference reflectometry (GNSS-IR) research, only the frequency of signal-to-noise ratio (SNR) oscillations has been used to estimate sea-level height. However, the characteristic parameters of SNR oscillations are not isolated from each other, and a single feature cannot accurately and comprehensively capture the environmental changes of reflecting surface. Our simulation results show that for the nonlinear least squares (NLS), when there is a certain difference between the fitting frequency and the actual frequency of SNR oscillations, the deviation of the phase solution obtained is approximately linear with the frequency difference. Consequently, a linear phase correction GNSS-IR sea-level estimation method is constructed in this study. This method integrates the Lomb–Scargle periodogram (LSP) and NLS to process SNR oscillations, using the phase obtained from NLS to correct the retrieval error of LSP. Through processing SNR data from four sites for nearly half a year, we verified the stability of the relationship between phase and frequency-based retrieval error at different sites in continuous monitoring, and established the relationship model between the two. Then, utilizing the relationship model acquired at different sites, we estimated the sea-level variations for the next 6 months at each site through joint frequency and phase versus reflector height relationships. Experimental results show that the phases acquired from NLS can effectively correct the retrieval error of LSP. Compared with the traditional method using only frequency, the root mean square error and mean absolute error of the retrieval results obtained from the linear phase correction GNSS-IR sea-level estimation method based on LSP-NLS are both reduced by about 60%. This multi-feature fusion technique introduces a new perspective and technical approach for GNSS-IR sea-level estimations. [ABSTRACT FROM AUTHOR]