A method for counting goods inventory and a system thereof, applied to an automatic vending container, the automatic vending container is provided with N cabinets (10), the method includes: arranging an independent RFID reader (20, 430) in each cabinet (10); at a first start time instant, starting one RFID reader (20, 430) to scan an RFID tag (100); at a second start time instant, starting another RFID reader (20, 430) to scan an RFID tag (200); repeating the operations until an N^thstart time instant, and starting a last RFID reader (20, 430) to scan an RFID tag (300); wherein the first start time instant to the N^thstart time instant are all a time instant within an inventory counting time period, and a random time interval is defined between adjacent start time instants. Inventory counting of all the goods is completed by arranging an independent RFID reader (20, 430) in each cabinet (10) based on RFID technology. With the method for counting goods inventory, the RFID reader does not need to be manually moved, and fully automatic operation is practiced. Inventory counting is performed and data is uploaded in a remote control manner.