Network coding is a promising technique to improve the throughput performance of wireless networks. In this paper, we propose a novel network-coding-based hybrid retransmission request protocol for two-way relaying system. The proposed protocol can retransmit more information in a given time interval by introducing network coding in the retransmission process, thus improving the throughput. Furthermore, we derive the frame error rate and delay performance using the L-ary pulse amplitude modulation by solving Markov state transition equations. Applying these results, the closed-form approximate solution of the throughput is acquired. Numerical results have validated our analytical results, and demonstrated that the proposed protocol outperforms the traditional hybrid retransmission request protocol for two-way relaying system by a throughput gain of about 9% when the relay lies close to the midpoint of the two users.