The invention discloses a food safety traceability intelligent warehousing system and a method for operating the warehousing system, belonging to the technical field of food safety traceability, Including front gantry, Rear gantry, Intelligent shelf and storage robots, a single chip microcomputer is arranged in the intelligent shelf, UPS power supply module, IPC Industrial Computer, Virtual Server, Local servers and local embedded databases, the IPC industrial computer is connected with the sound and light alarm module respectively, The voice broadcast module, the data display module and the handheld mobile terminal are connected; the local server is connected with the ONS solver and the inquiry server respectively; the ONS solver is connected with the ONS infrastructure module; the inquiry server is connected with the PML server; and the local embedded database is connected with the cloud server. The invention realizes automatic allocation of storage space, automatic identification ofproducts, inventory counting, automatic alarm, high intelligent degree, low management cost and easy popularization through RFID technology.