The present invention relates to an electron bean injection control of a mass spectrometer. A mass spectrometer of the present invention includes: a reference waveform generator configured to generate a reference waveform signal having one type of a square wave and a sine wave, a waveform generator configured to generate a sync signal synchronized with the reference waveform signal; an RF module configured to generate an RF voltage signal from the reference waveform signal and apply the RF voltage signal to an RF electrode in the ion trap, an electron beam generator configured to control an operation of an ultraviolet (UV) diode for generating an electron beam injected into the ion trap according to an input control signal, and a control circuit configured to generate the control signal by using the square wave signal.