An array-based ion storage system includes an ion generation section, and an ion storage section having a first end electrode coupled to the ion generation section and having multiple holes, a second end electrode having multiple holes, an intermediate electrode having multiple holes, a first insulator formed as a ring between the first end electrode and the intermediate electrode, and a second insulator formed as a ring between the intermediate electrode and the second end electrode. The ion storage section can be made thinner to facilitate consistency in ion extraction and reduce the spread of an ion mobility spectrum peak. The insulators have a big hole, and the ions cannot bump onto the insulation material during ion vibration or thermal movement in the storage space. Therefore, charge transfer and accumulation at the insulator and the subsequent discharge will not occur, suppressing instability of storage and loss of ions.