In-orbit long-term performance of GNSS (Global Navigation Satellite System) clocks is being estimated with respect to the monitoring information of the phase comparisons between the main clock and the redundancy. In the satellite clock generator, the time-difference against each other for the onboard main clock and the redundancy is sampled continuously as monitoring information. The monitoring information is transmitted down to ground. The receiver on the sensor station demodulated the monitor information. Data processing is operated on the time-difference of on-board clocks and the long-term property of on-board clocks can be estimated. The proposed technique is considered to be simple, fast and need not require special time-frequency test equipment. Comparing to the ground measurements, a very good agreement can be obtained with the proposed technique.