Energy spectrum is one of the best important methods for the nuclear radiation analysis. The nuclear pulse received by the detector is translated into electrical signal and sent into ADC after shaping, followed by processing of the MCU and output of the spectral data. The higher sampling rate can detect the more accurate nuclear signal and achieve higher energy resolution. But high sampling rate and sample bits cannot have both. Multiplexing technique is proposed to control multiple 16 bits ADCs sampling parallel to realize a higher sampling rate. Based on the NI USB7845R Multifunction RIO Card, the multichannel spectrum analysis system with 1 M/s sampling rate is realized by combination of two 500 k/s ADC, the system performance and the stability all are verified in this paper. The experimental results show that the multiplexing technology can be used to improve both the sampling rate and the energy resolution of the energy spectrum analysis system under the condition of without changing the hardware circuit.