At present, our society is more and more interested in innovation ability. The Chinese government emphasizes higher education institutions' role in forming and developing students' innovation abilities. However, few studies have explored how to improve the innovation ability of higher education students from the academic atmosphere of higher education institutions. This study examines the impact of the academic atmosphere on Chinese graduate students' innovation ability and the chain mediating effect of scientific research self-efficacy and scientific engagement. Three hundred thirteen Chinese postgraduates were investigated with the academic atmosphere scale, scientific research self-efficacy scale, scientific engagement scale, and innovation ability scale. The bootstrap method was used to test the mediating effect. The results show that (1) there is a significant positive correlation between the academic atmosphere and the innovation ability of graduate students, (2) scientific research self-efficacy and scientific engagement play a mediating role between the academic atmosphere and graduate students' innovation ability, and (3) the mediating role includes three paths: the mediating role of scientific research self-efficacy, the mediating role of scientific engagement, and the chain mediating role of scientific research self-efficacy and scientific engagement. The research results provide empirical evidence and reference suggestions for improving the innovation ability of graduate students. Therefore, this study suggests that higher education institutions should adopt more effective academic atmosphere management strategies to create a positive academic atmosphere to improve the scientific research efficacy and engagement of postgraduates and thus solve the practical problem of the low innovation ability of postgraduates.