Abstract: To resolve the problem of the tree-based anti-collision algorithm which produces many idle time slots and invalid collision time slots in the RFID system, an anti-collision algorithm based on Coding and Jumping Tree(CJT) structure is proposed. By coding tag ID information and determining tag prefix in the system, the inquiry command was optimized; when the collision happens, judging whether the R sequence was the same, detecting the validity of collision, put the ID codes for effective collision into the stack and skipping invalid collision. Simulation results show that the new algorithm avoids idle time slots, reduce the number of collision time slots, then can lower the delay of tag identification and improve the throughput of the system up to 0.625.