A method of controlling a mass spectrometer comprises the steps of: supplying a current to a cathode electrode of an ion source having the cathode electrode and an anode electrode, and ionizing a molecules of a gas to be measured; selecting ions generated in the ion source by mass-to-charge ratio; and detecting an ion current value of the selected ions. When a partial pressure of the gas to be measured is measured based on a detection result of the ion current value, a cathode current is supplied to the cathode electrode such that an emission current flowing between the cathode electrode and the anode electrode becomes constant. When a partial pressure of the gas to be measured is not measured, a constant current having a current value less than that of the cathode current is supplied to the cathode electrode.