A 3-channel nuclear signal measurement and analysis system of 252Cf spontaneous fission neutron source which is based on the embedded FPGA is constructed. All the signals from 3 channels are captured synchronously and we obtained all the time- and frequency-dependant signatures, such as the temporal autocorrelations of each channel, cross-correlation between two different channels, auto power spectrum of each channel, cross power spectrum between two different channels. The experimental results show that the FPGA-based processing speed is 7 times faster than PC-based and the error between two different schemes is almost negligible which means that embedded frequency spectrum analysis method is effective.