We have developed a method for determining the orientations of the principal axes of an ion trap using an ion matter-wave interferometer. By examining the ion matter-wave interference signal induced by spin-dependent momentum kicks originating from stimulated Raman transitions, we can accurately ascertain the angles between the directions of these momentum kicks and the trap principal axes. The application of direct–current voltage to the ground electrodes, a common method adopted to finely tune trap frequencies in ion traps, leads to the trap principal axes rotating, a phenomenon that is yet to be reported quantatively. Our measurements successfully captured the rotation of the trap axes depending on the applied offset voltages. The findings of this study offer valuable insights into the functioning of ion traps for diverse quantum science and technology applications.