Ship-borne global navigation satellite system (GNSS) technique can overcome the weakness of satellite altimetry and tide gauge in measuring sea surface heights (SSHs) over coastal seas. Ship-borne GNSS technique can be used to calibrate SSHs determined by the satellite altimetry and tide gauge. The ship-borne GNSS data are processed with the single-epoch precise point positioning (PPP) method to estimate SSHs which are filtered by the Gaussian filter to weaken and/or remove effects of sea wind and wave field. Tidal corrections are also taken into consideration to improve SSHs. One crossover adjustment method is put forward to calculate the bias and drift along the ship route and assess the accuracy of SSHs. We processed the in-situ ship-borne GPS data over the offshore sea around Keelung to compute precisely SSHs with the single-epoch PPP. Statistical results of SSH differences of crossover points indicate that the root mean squares error of SSHs determined by the ship-borne GPS is up to level of 12.9 cm over the offshore sea ~30 km far away to land.