This paper proposes a new frequency synchronization algorithm based on alternating guard intervals in the TDS-OFDM system. It utilizes the following two facts: the maximum length of identical sequences exist in the alternating guard intervals in the TDS-OFDM system and high precise frequency estimation can be achieved by extending the equivalent length of the delay for autocorrelation in the conventional frequency synchronization algorithm. The variance of the frequency estimation over a typical DTTB multi-path channel in the proposed algorithm is dramatically decreased from 10-8 , in the conventional algorithm, to 10-13. The proposed algorithm is also robust against timing errors as verified by the simulation results. In addition, much lower hardware complexity can be achieved.