An atmospheric pressure ionization mass spectrometer having a multi-stage differential pumping system including one or more intermediate vacuum chambers (6, 9) between an ionization chamber for generating ions under atmospheric pressure and an analysis chamber for mass-separating and detecting the ions under high vacuum, wherein: either a partition wall separating the ionization chamber and a neighboring first-stage intermediate vacuum chamber, or an exit end of an ion introduction part for making these two chambers (1, 6) communicate with each other, is used as a first electrode; an entrance part of a skimmer electrode between the first-stage intermediate vacuum chamber and either a second-stage intermediate vacuum chamber or an analysis chamber is used as a second electrode; and an ion transport electrode for creating an electric field for transporting the ions while converging them is provided in the first-stage intermediate vacuum chamber, and the atmospheric pressure ionization mass spectrometer further comprising: a) a first voltage setting section (21, 22) for setting voltages (V DL, V QDC) individually applied to the first electrode and the ion transport electrode, to adjust a direct-current potential difference between these two electrodes (3, 7) so that a background noise on the measured spectra, which is caused by cluster ions, is reduced; and b) a second voltage setting section (22, 23) for setting voltages (V QDC), individually applied to the ion transport electrode and the second electrode, to adjust a direct-current potential difference between these two electrodes (7, 8) according to whether or not a collision induced dissociation mode is selected as the analyzing mode. either a partition wall separating the ionization chamber and a neighboring first-stage intermediate vacuum chamber, or an exit end of an ion introduction part for making these two chambers (1, 6) communicate with each other, is used as a first electrode; an entrance part of a skimmer electrode between the first-stage intermediate vacuum chamber and either a second-stage intermediate vacuum chamber or an analysis chamber is used as a second electrode; and an ion transport electrode for creating an electric field for transporting the ions while converging them is provided in the first-stage intermediate vacuum chamber, and the atmospheric pressure ionization mass spectrometer further comprising: a) a first voltage setting section (21, 22) for setting voltages (V DL, V QDC) individually applied to the first electrode and the ion transport electrode, to adjust a direct-current potential difference between these two electrodes (3, 7) so that a background noise on the measured spectra, which is caused by cluster ions, is reduced; and b) a second voltage setting section (22, 23) for setting voltages (V QDC), individually applied to the ion transport electrode and the second electrode, to adjust a direct-current potential difference between these two electrodes (7, 8) according to whether or not a collision induced dissociation mode is selected as the analyzing mode. a) a first voltage setting section (21, 22) for setting voltages (V DL, V QDC) individually applied to the first electrode and the ion transport electrode, to adjust a direct-current potential difference between these two electrodes (3, 7) so that a background noise on the measured spectra, which is caused by cluster ions, is reduced; and b) a second voltage setting section (22, 23) for setting voltages (V QDC), individually applied to the ion transport electrode and the second electrode, to adjust a direct-current potential difference between these two electrodes (7, 8) according to whether or not a collision induced dissociation mode is selected as the analyzing mode.