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Estimating sea surface height (SSH) based on Global Navigation Satellite System (GNSS) signal measurements in the presence of a rough sea surface is a challenging problem. This paper presents a model-free SSH estimation method to handle this challenging problem. The concept of power ratio is introduced that is defined as the ratio of the correlation power at the desired code phase over the peak correlation power. This desired code phase corresponds to the peak correlation power of reflected signal when the sea surface is perfectly smooth. A power-ratio-based method is presented to estimate the delay of the reflected signal relative to the direct signal, which is then used to estimate the SSH. Two cost functions are defined to estimate the desired power ratio and the SSH through minimizing the cost functions. A low-altitude airborne experiment was conducted and both direct and reflected GNSS signals were collected. The airborne experimental data were processed to generate delay waveforms (correlation power versus code delay). Applying the experimental data to the proposed method demonstrated that the error of mean SSH estimation can be of the order of decimeter in the presence of significant wave height of about 4 m. The main advantage of the proposed method is that it does not require any a priori knowledge of the sea state information or any theoretical model. Thus, the proposed method is not affected by the modeling errors or uncertainties.