The organizational system is directly associated with overall organizational management and sustainability. The reason is that the organizational system has a strong relationship with organizational performance. One of the most important functions of the organizational system is the high-performance work system, which is the system that manages the employees so that they can maximize their functions, this study focuses on the importance of a high-performance work system in order to achieve organizational goals and increase performance. In particular, a high-performance work system is directly related to innovation performance that secures the competitive advantage of organizations. Based on such background, this study focused on how a high-performance system improves innovation performance. Unlike previous studies, rather than simply focusing on variables exploration or main effect verification, we provided and verified the research model related to the process by which innovation performance occurs. Specifically, this study aimed to investigate whether high-performance work systems in organizations enhance employees’ innovation performance and examined the mediating role of employees’ intrinsic motivation in enhancing innovation performance. In addition, we investigated the moderating role of employee person–organization fit in high-performance work systems and employee intrinsic ation directly. To validate this model, we collected data from 309 members of Chinese SMEs. We found that high-performance work systems positively affect employees’ innovation performance through a person–organization fit and that employees’ person–organization fit significantly moderates the relationship between high-performance work systems and employees’ intrinsic motivation directly. Overall, this study expands the scope of research on the enhancement of employee innovation performance and provides a theoretical basis for related research, which is also a contribution of this study.