The invention relates to a vehicle safe box device applying NFC and a running method thereof. The vehicle safe box device comprises: an NFC module disposed in an in-vehicle glove box, and for applying NFC authentication of the door of the glove box along with a vehicle car of a driver; and a BCM detecting whether a door of a driver's seat is open or not according to a normal procedure, and determining whether a loudspeaker alarm to be sent or not and whether the door of the glove box to be opened or not based on the authentication application result and the detection result of whether the door of the driver's seat is open or not of the NFC module. According to the vehicle safe box device applying NFC and the running method thereof, when the glove box is forced to open under the state that NFC authentication fails to pass, the alarm is given to reinforce burglary prevention so as to prevent burglary accidents, and especially when the vehicle is robbed or stolen, stability of the glove box is reinforced, and privacy of the driver is protected from being exposed to persons in the same vehicle.