For the Single-Carrier Frequency-Domain Equalization system(SC-FDE), a SNR estimation algorithm based on the repetitive sequence DFT is proposed. The simulation results show that the proposed algorithm can effectively improve the performance and the standard deviation of SNR estimation is only 23.2% of the result base on the traditional correlation method when SNR is 20 dB. The SC-FDE using the proposed algorithm can get 0.06 dB SNR gain than the original algorithm. Further, the system FER will decrease and stabilize with the increase of the number of UW blocks. The number of UW blocks is determined to be eight to balance FER, time delay and storage which has only 0.02dB loss compared to using more blocks.