The present invention relates to an apparatus and method for controlling a pipeline-type ion cyclotron resonance mass spectrometer, in which an ion trap unit of the ion cyclotron resonance mass spectrometer is capable of using two digitizers at the same time, thus enabling a measurement process for detecting an electrical signal which indicates the mass of ions corresponding to a specific purpose, and another measurement process for detecting another electrical signal which indicates the mass of ions corresponding to another specific purpose, to be simultaneously performed. Accordingly, it is an aim of the present invention to provide an apparatus and method for controlling a pipeline-type ion cyclotron resonance mass spectrometer, which can overcome the problems of time delay among control procedures, and can present a signal detection step wherein an excitation electrode is utilized to improve the sensitivity and speed of signal detection.