The invention discloses a field emission device structure integrated with an ion collection electrode and an application method thereof. The device structure comprises a cathode, a first insulating layer, an electron emission control electrode, a second insulating layer and an ion collection electrode which are stacked sequentially from bottom to top, wherein the ion collection electrode is a flatelectrode with a plurality of micropores, and the diameter of the micropore is 1.5 to 3.5 mum; the cathode, the first insulating layer, the electron emission control electrode and the second insulating layer protrude upwardly in the micropore to form a surrounding structure in a sleeving mode from inside to outside and from bottom to top sequentially; the electron emission control electrode in the micropore is higher than the plane of the ion collection electrode, a volcanic vent-like gate hole is formed, and the top end of the gate hole and the plane of the ion collection electrode have a height difference more than 300 nm; and the cathode in the micropore is located in the electron emission control electrode gate hole and is not higher than the top end of the gate hole. When the devicestructure works, the electron emission control electrode applies positive bias and the ion collection electrode applies negative bias.