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In GNSS systems,frequency stability of satellite on‐board clock will affect satellite clock offset modeling and prediction,and then impact the accuracy of positioning and timing,so frequency stability estimation of satellite on‐board clock is of great significance for GNSS systems.This paper proposes a frequency stability estimation method for BDS GEO on‐board clock based on satellite transponded carrier doppler.Frequency offset of on‐board clock is estimated by self‐transmitting and self‐receiving transponded carrier doppler of ground station,and then the frequency stability can be estimated.Theoretical realization principle of the method is analyzed,and is validated using BDS observation.Experimental show that frequency stability estimation results of this method are basically consistent with that of network method and the relative deviation is less than 10% within average interval of 1000s.