The interest in a precise orbit determination (POD) of Low Earth Orbiters (LEOs) especially in pure geometrical mode only based on GNSS (Global Navigation Satellite System) observations has been rapidly grown. The geometrical absolute positions of LEO can be estimated based on carrier phase SST (Satellite to Satellite Tracking) observations with an accuracy of cm. However, limiting factor for LEO POD is mainly encountered with the modeling of the carrier phase observations, where a phase center location of the GNSS antenna is a pre-requisite for precise determination of LEO orbit. Based on robot calibration, the absolute phase center (PC) and its variation (PCV) are estimated for a number of GNSS receiver antennas. It should be mentioned that for the GNSS transmitter antennas, the absolute phase centers and their variations are estimated based on GNSS data post-processing. Nowadays, the Earth gravity field recovery missions are equipped with non-geodetic receiver antennas, which the phase centers and their variation before launch are determined based on robot calibration strategy. After mission launch, the empirical antenna phase center and phase center variation should be estimated based on GNSS carrier phase observations to improve accuracy LEO orbit. In this paper, different methods to estimate phase center variation are introduced, applied to the twin GRACE and GOCE observations and improvements on POD will be discussed.