The choice of the accurate and proper signal is the key to enhance the sensitivity and contrast of ultrasound-modulated optical tomography（UOT）. Fast Fourier transform (FFT) is used in the digital frequency analysis of modulation signal. Spectral intensity of zero frequency (I0) represents the unmodulated light intensity, and the sum total of spectral intensity (If) from 0.2 MHz to 1.8 MHz depended on the frequency range of ultrasonic probe represents the ultrasound-modulated light intensity. Compared with the in-time signal, If has the higher sensitivity to optical properties of media, but it is easy to be influenced by the non-target media. The modulated depth of in-frequency signal (M2=If/I0) is not easy to be influenced by non-target media, but it has low sensitivity to optical properties of the target media. The results indicate that the result of in-frequency signal is not better than the in-time signal for image reconstruction and processing.