Second-order scattering based wave height measurement with high-frequency (HF) radar has always been subjected to problems such as distance limitation and external interference especially under low or moderate sea state. The performance is further exacerbated for a compact system with small antennas. First-order Bragg scattering has been investigated to relate wave height to the stronger Bragg backscatter, but calibrating the echo power along distance and direction is challenging. In this paper, a new method is presented to deal with the calibration and improve the Bragg scattering based wave height estimation from dual-frequency radar data. The relative difference of propagation attenuation and directional spreading between two operating frequencies has been found to be identifiable along range and almost independent of direction, and it is employed to effectively reduce the fitting requirements of in situ wave buoys. A 20-day experiment was performed over the Taiwan Strait of China to validate this method. Comparison of wave height measured by radar and buoys at distance of 15 km and 70 km shows that the root-mean-square errors are 0.34 m and 0.56 m, respectively, with correlation coefficient of 0.82 and 0.84.