Based Correctly handling the creativity of employees who have not been adopted is not only conducive to continuously stimulating employees’ creativity and improving individual innovation performance, but also conducive to making the best use of organizational resources. This study integrates conservation of resource theory (COR) and social information processing theory to explore the influence of bootleg innovation behavior in organizations on individual innovation performance, as well as the mediating role of cognitive flexibility and the moderating role of leadership emotional intelligence. A three-stage time-lagged research design is used to obtain a valid sample of 327 employees from China. The PROCESS macro for SPSS was applied to test the hypothesized relationships. Findings demonstrated that bootleg innovation is positively related to individual innovation performance; cognitive flexibility mediates the relationship between bootleg innovation and individual innovation performance. Moreover, leadership emotional intelligence moderates the relationship between bootleg innovation and individual innovation performance and between bootleg innovation and cognitive flexibility and between cognitive flexibility and individual innovation performance respectively. The conclusion of the study not only provides a theoretical basis for individuals and leaders to deal with employees’ creative abortion, but also provides a new thinking mode for how to maximize the effectiveness of unaccepted ideas and promote individual innovation performance.