Employee innovation behavior is an important part of shaping an organization's competitive advantage. Although previous studies have shown that leadership style can significantly affect employee innovation behavior, little is known about the mechanism and boundary conditions between the two. Based on the effective questionnaire data of 422 employees in domestic new energy industry, a moderated mediating effect model is constructed and tested. The empirical results show that: inclusive leadership has a significant positive influence on employee innovation behavior; organizational harmony can mediate the relationship between inclusive leadership and employee innovation behavior; organizational innovation atmosphere plays a positive moderating role between inclusive leadership and organizational harmony. When the atmosphere of organizational innovation becomes stronger, the impact of inclusive leadership on organizational harmony grows higher. The research model of this paper explains the mechanism of inclusive leadership on employee innovation behavior, which not only opens the “black box” between them, but also provides management enlightenment and countermeasures and suggestions on how to effectively enhance the innovative behavior of employees in the organization.