Discrete Fourier transform-spread generalized multi-carrier (DFT-S-GMC) based single carrier-frequency division multiple access (SC-FDMA) scheme is a promising solution for uplink transmission of broadband wireless communication. In this paper, the impact of non-perfect orthogonal prototype filter to the performance of the DFT-S-GMC system is discussed. Single sub-band frequency-domain equalization (FDE) method is presented and the performance loss caused by FDE-tone discarding is analyzed. Moreover, the post-processing signal to interference plus noise ratio (SINR) of DFT-S-GMC receiver over multi-path channel is addressed. The theoretical analysis illustrates that the non-perfect orthogonal prototype filter results in inter-symbol interference (ISI) and inter-sub-band interference (IBI), and the variance of the ISI is still less than 1e-4 and much larger than that of IBI. By designing proper system parameters, the reconstruction error due to FDE-tones discarding can be controlled under -40 dB; the post-processing SINR of the DFT-S-GMC receiver with minimum mean square error (MMSE) equalization is higher than that with zero forcing (ZF) equalization. The theoretical performances are verified by extensive simulation results. Discrete Fourier transform-spread generalized multi-carrier (DFT-S-GMC) based single carrier-frequency division multiple access (SC-FDMA) scheme is a promising solution for uplink transmission of broadband wireless communication. In this paper, the impact of non -perfect orthogonal prototype filter to the performance of the DFT-S-GMC system is discussed. Single sub-band frequency-domain equalization (FDE) method is presented and the performance loss caused by FDE-tone discarding was analyzed. The theoretical analysis illustrates that the non-perfect orthogonal prototype filter results in inter-symbol interference (ISI) and inter- sub-band interference (IBI), and the variance of the ISI is still less than 1e-4 and much larger than that of IBI. By designing proper system parameters, the reconstruction error due to FDE-tones discarding can be controlled und er -40 dB; the post-processing SINR of the DFT-S-GMC receiver with minimum mean square error (MMSE) equalization is higher than that with zero forcing (ZF) equalization. The theoretical performances are verified by extensive simulation results.