With the development of wireless technologies, wireless relay systems have become a popular topic. To design practical wireless relay systems, link adaptation is an important technique. Because there are both broadcast and multiple access channels in wireless relay systems, link adaptation is difficult to design and hence the optimal throughput is hard to achieve. In this study, a novel method is proposed to maximize the system throughput of wireless relay systems by utilizing the most popular link adaptation methods, adaptive modulation and coding (AMC) and hybrid automatic repeat request (HARQ). The proposed method utilizes the characteristics and operations of AMC and HARQ to adaptively adjust the thresholds for selecting modulation and coding scheme (MCS) to be used. Thus the system can keep tracking the optimal values of the thresholds. Therefore, the system throughput can be maximized. We set up simulations for different relay environment settings, such as different relay HARQ protocols, placements, and multiplexing schemes, to verify the capability of the proposed method. The simulation results show that, compared to the existing method, the proposed method indeed improves system throughput under a variety of relay settings and can be easily applied to different system platforms.