Non-contiguous OFDM (NC-OFDM) system is popular as its characteristics of avoiding interference by licensed users detection in Cognitive Radio (CR) text. Some traditional channel estimation methods can not be applied to the NC-OFDM systems directly as its non-contiguous subcarrier. The improved timedomain channel estimation method which is different with the traditional LS and DFT channel estimation methods is proposed in this paper. It adopted the spectrum sensing based on CR context at the transmitter and receiver before the IFFT block and after the FFT blocks, respectively. The simulation results verify that the mean square error (MSE) and bit error rate (BER) performance outperform than those of the conventional schemes under the same condition.