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In this paper, a joint carrier synchronization and equalization algorithm is proposed for OFDM systems in the tracking stage. Significantly, the carrier synchronization scheme is a dual-loop, which is composed of an outer and an inner loops, with the multirate processing to eliminate the carrier frequency offset and the channel phase variation. In addition, the gain equalization loop is employed to compensate the magnitude distortion on each subchannel in the frequency domain. Based on MMSE criterion, the cost function of the joint algorithm is presented to minimize the decision error on each subchannel and, further, lower the uncoded BER concurrently. Besides, the subchannel SDR is derived in terms of the powers of the phase and gain jitters. Considering a figure of merit for CFO RMS error, the improvement for the joint algorithm is about 1-order at least compared with the considered algorithms. According to BER derivation and simulation in an AWGN channel, SNR losses at BER=10-6 from the theory to the derivation and simulation of the proposed algorithm are about 0.1 dB (derivation) and 0.4 dB (simulation). The proposed joint algorithm can estimate and compensate the carrier frequency offset as well as channel distortion accurately.