Single-carrier modulation has been applied widely in wireless systems. However, the traditional time domain equalization (TDE) based on the direct decision feedback equalization is complex, especially when SC and multi-carrier are compatible in a system. In this paper, a novel frequency domain equalizer (FDE) is proposed for the PN-based SC system. This method can simplify the calculation based on LMS algorithm and the PN extension is used to initialize DFE, which have advantages in the convergence speed. Simulation results show that a significant improvement in terms of BER is expected for the new method compared with the linear FDE. Moreover, this method can share the same block diagram and common functions with OFDM system.