As an important equipment for sea state remote sensing, high frequency surface wave radar(HFSWR) has received more and more attention. The conventional method for wave height inversion is based on the ratio of the integration of the second-order spectral continuum to that of the first-order region, where the strong external noise and the incorrect delineation of the first- and second-order Doppler spectral regions due to spectral aliasing are two major sources of errors in the wave height. To account for these factors, two more indices are introduced to the wave height estimation, i.e., the ratio of the maximum power of the second-order continuum to that of the Bragg spectral region(RSCB) and the ratio of the power of the second harmonic peak to that of the Bragg peak(RSHB). Both indices also have a strong correlation with the underlying wave height. On the basis of all these indices an empirical model is proposed to estimate the wave height. This method has been used in a three-months long experiment of the ocean state measuring and analyzing radar, type S(OSMAR-S), which is a portable HFSWR with compact cross-loop/monopole receive antennas developed by Wuhan University since 2006. During the experiment in the Taiwan Strait, the significant wave height varied from 0 to 5 m. The significant wave heights estimated by the OSMAR-S correlate well with the data provided by the Oceanweather Inc. for comparison, with a correlation coefficient of 0.74 and a root mean square error(RMSE) of 0.77 m. The proposed method has made an effective improvement to the wave height estimation and thus a further step toward operational use of the OSMAR-S in the wave height extraction. As an important equipment for sea state remote sensing, high frequency surface wave radar (HFSWR) has received more and more attention. The conventional method for wave height inversion is based on the ratio of the integration of the second-order spectral continuum to that of the first-order region, where the strong external noise and the incorrect delineation of the first- and second-order Doppler spectral regions due to spectral aliasing are two major sources of errors in the wave height. To account for these factors, two more indices are introduced to the wave height estimation, ie, the ratio of the maximum power of the second-order continuum to that of the Bragg spectral region (RSCB) and the ratio of the power of the second harmonic peak to that of the Bragg peak ( Both the indices of have a strong correlation with the underlying wave height. On the basis of all these indices an empirical model is proposed to estimate the wave height. This method has been used in a three-months long experiment of the ocean state measuring and analyzing radar, type S (OSMAR-S), which is a portable HFSWR with compact cross-loop / monopole receive antenna developed by Wuhan University since 2006. During the experiment in the Taiwan Strait, the significant wave height varied from 0 to 5 m. The significant wave heights estimated by the OSMAR-S correlate well with the data provided by the Oceanweather Inc. for comparison, with a correlation coefficient of 0.74 and a root mean square error (RMSE) of 0.77 m. The proposed method has made an effective improvement to the wave height estimation and thus a further step toward operational use of the OSMAR-S in the wave height extraction.