The data acquisition system is based on ROOT and waveform digital technology, including neutron detector, waveform digitizer, PCI card, optical fiber, computer, reaction target device, stepper motor, data acquisition software and control target software. It achieves to acquire and record the waveform information of signal measured by the detector using a waveform digitizer. The specific target position is changed by the stepper motor which is remotely controlled by the data acquisition software and control target software. It is implemented by the exchange of information between the data acquisition software and the control target software. The system realizes to automatically open files and change targets at fixed intervals. It is capable of data compression by removing the data those are not signals, and automatic alarm when the beam is lost.