Purpose This paper aims to explore the impact of flexible human resource management system (FHRMS) on employee innovation performance in Chinese context. The boundary conditions of employability and organizational identity are also discussed. Design/methodology/approach This study is based on 322 questionnaire survey from employees in China. The questionnaires were collected at two time points. This study used the method of multi-level linear model analysis for empirical test. Findings This study has three conclusions. First, FHRMS have a significant positive impact on employee innovation performance, with employability playing a mediating role. Second, organizational identity plays a moderating role between employability and employee innovation performance. Third, organizational identity moderates the mediating effect of a human source management systems on employee innovation performance through employability. Originality/value The results are helpful to open the “black box” of the influence of FHRMS on employees’ individual innovation performance. This study provides a reference for enterprises to establish flexible human source management system to improve employee innovation performance.