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Because the DFT-based channel estimation method could not slove the degradation of performance caused by the energy leakage from non-sample locations of the multipath timing, we research on a channel estimation method by adding virtual channel frequency response (VCFR) [7]. However, this VCFR method cannot adapt to the complicated situations of the uplink reception for LTE Physical Uplink Shared Channel(PUSCH). Owing to the above issue, an improved method which adopts a novel frequency window function and a new noise reduction strategy is presented. The superiority of the proposed method over other VCFR channel estimation methods is verified in performance and flexibility to various multipath fading channels. So it is widely used in wireless communication system. Theoretical analysis and simulation experiments show that this method can effectively improve the channel estimation accuracy and system performance. It can also improve the system error rate about 2 dB and the throughput of the system can also improve about 4 dB than the 3GPP requirement.