In this paper, we develop a novel hybrid automatic-repeat-request(ARQ) protocol for the quan-tum communication system using quantum stabilizer codes. The quantum information is encoded by sta-bilizer codes to against the channel noise. The two-photon entangled state is prepared for codeword se-cure transmission. Hybrid ARQ protocol rules the recognition and retransmission of error codewords. In this protocol, the property of quantum entangled state ensures the security of information, the theory of hy-brid ARQ system improves the reliability of transmis-sion, the theory of quantum stabilizer codes corrects the flipping errors of codewords. Finally, we verify the security and throughput efficiency of this protocol.