Superconducting quantum interface devices (SQUID) is widely used in human brain signal detection. As one of the applications of magnetoencephalography (MEG) system, the detection of the auditory evoked response is useful for the development of MEG system and the research into auditory mechanism of human brain. Generally, the auditory evoked response includes three peaks which are P50m, N100m and P200m. We develop a single-channel MEG system in a magnetically shielded room based on the superconducting quantum interface device (SQUID) and second-order axial gradiometer. The responses of the main peak N100m under different tone frequencies are preliminarily studied by using our system. The typical evoked response of N100m to 1 kHz pure tone and 100 ms duration is measured to be 0.4 pT. Under the tone stimulus at low frequency, the delay of the peak N100m to the tone onset is 125 ms at 100 Hz, which is longer than the typical value of 100 ms. In comparison with the response to 1 kHz pure tone stimulus, the amplitude of the evoked response in a random frequency range from 1 kHz to 4 kHz is stronger and the delay is several milliseconds. This work lays the foundation of the studies of the auditory mechanism and multichannel MEG system by using software gradiometers.