The present invention discloses a communication system with a data-dependent superimposed training mechanism and a communication method thereof. The system uses a precoding module installed in front of the data-dependent superimposed training mechanism to precode data by a precoding matrix. The precoding matrix is a N×N unitary matrix, which is constructed by Q×Q precoding sub-matrix. Q is the block size N divided by the channel length. The precoding matrix can achieve full frequency diversity. Any two sets of data precoded by the precoding matrix must be different from each other, such that the receiver can effectively identify the data transmitted from the transmitter and the computational complexity of the receiver is reduced.