An intelligent storage system and an intelligent storage method thereof are disclosed. The system includes a cabinet and loading tables, each loading table includes an accommodating groove having a shape corresponding the shape of the object to be stored, and a sensing device in the accommodating groove. A central control device includes a processor electrically connected to the sensing device, the output device and an input device, and a system database for the processor to access or store information. The sensing devices senses whether there is a corresponding stored object in each accommodating groove to form a status signal carrying an identification code, and outputs it to the processor, then the processor accesses the corresponding information in the system database according to the identification code of the status signal, so as to realize the management and status display of the stored object, and effectively improve work safety and effectiveness.