The invention discloses a RFID indoor positioning system based on the depth perception and an operating method thereof. The system comprises a RFID reader, RFID external antennas and passive RFID tags. RFID external antenna arrays and reference tag arrays are arranged in the space properly, the reference tags carried by a target object are positioned through a power hopping and feedback correction mechanism, and the position of the target object can be estimated. The method is characterized in that on the basis of the depth perception, aiming to the features of the passive RFID tags, deep data are sensed through two varieties of multi-dimensional and deep systems, and an accurate and real-time indoor positioning mechanism is provided. In the spatial dimension, the system performance is improved through layer-crossed perception and parameter optimization; in the time dimension, the system corrects the accuracy of next positioning by collecting feedback data in an adaptive manner.