Global navigation satellite system-reflectometry (GNSS-R) has great potential to be a novel technique for altimetry, which can be used to derive sea surface heights (SSH). Shipborne altimetry is an important method to measure local SSH with high spatial resolution. In order to test the feasibility of shipborne dual-antenna GNSS-R reflector height retrieval, we developed a GNSS-R receiver system and performed experiments on a research vessel. In this study, direct and reflected GPS/BDS signals were collected using the same setup, and processed to estimate the reflector heights on the basis of path-delay measurements. A strategy of obtaining the GPS/BDS code-level path delay based on 10-ms coherent integration waveforms was adopted. We analyzed the relationship between the path-delay error and the error of the estimated reflector height, and we pointed out that the error in the path delay was amplified when the satellite elevation was low. We also performed reflector height retrieval based on BDS-3 signals for the first time. We evaluated the precisions of the BDS-R and GPS-R derived reflector heights with 30°and 50°cut-off elevations. The results show that the standard deviation of solutions at different cases is around 1.0 m and precisions are slightly better for a 50°cut-off angle compared with a 30°cut-off angle. In general, the mean values of different cases are close, with differences of several centimeters for the experiments.