This paper presents a frequency compensation technology which uses spectrum analysis. First this method uses cross power spectrum to measure the frequency response of the hardware input channel which is to be compensated H(k). Second, put the signal which output by the hardware input into FFT transform, and get the spectrum of the output signal, Yr(k); the frequency response which uses hardware input channel H(k) compensates on the spectrum of output signal Yr(k). Get the compensated spectrum Yc(k). Finally, get the compensated signal of time domain by IFFT transform.