Abstract: The height of shipborne meteorological sensor above water surface is a necessary parameter to predict the atmospheric refractive index profile by using the bulk aerodynamical method, which is of great significance to the radio meteorological parameter monitoring systems such as evaporation duct monitoring system. The Global Navigation Satellite System (GNSS) carrier-to-noise ratio (CNR) is extracted from the shipborne GNSS receiver output. The coherence of GNSS direct signal and reflected signal from water surface is analyzed using Lomb Scargle Periodogram to retrieve the height of the GNSS antenna phase center above reflection surface, and then the height of shipborne meteorological sensor is calculated indirectly. The proposed method was verified by barge experiments. Based on the statistics of the effective inversions, the sea state influence on the inversion results as well as the time-averaged variation of the inversion results is analyzed. It shows that the height of shipborne meteorological sensor can be effectively retrieved.