In deep space exploration, normal points FFT cannot exactly fulfill the frequency guide for very weak signals while very large size FFT cannot be computed by COTS. A parallel FFT method based on digital channelization is proposed to fulfill the frequency guide. The input signal is first divided into several narrow bands and FFT is computed in every sub-band. Then frequency estimation is performed by jointly detecting the valid sub-band spectrum lines. In FPGA implementation of the module equivalent to 29 points FFT，the FFT module is reused for resource saving. The test results show that the resolution is less than 10Hz when the sampling rate is 8MHz.