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Frequency domain equalization (FDE) has shown its ability to improve the performance of single carrier system. For DS-CDMA system, MMSE based FDE can obtain frequency diversity gain through undergoing more fading paths. Meanwhile, delay time-domain windowing technique has been introduced to suppress the noise power which perturbs the channel estimation. In this paper, we analysis the impact of delay time-domain windowing technique, the fading rate of the channel and the number of Rayleigh fading paths on the BER performance of DS-CDMA system with MMSE-FDE under MMSE channel estimation. Simulations show that delay time windowing technique can improve the BER performance significantly and such improvement grows with the increase of Eb/N0.