This study uses a hierarchical linear model (HLM) to examine the effects of cognitive ability and self-control on comprehensive academic performance among students in a high school in Beijing. The study included 572 participating students, including 291 boys and 281 girls, ranging in age from 16 to 18 years old. In this study, the individual level of students' cognitive abilities are used as the first-level variables, including memory ability (MA), information processing ability (IPA), representation ability (RA), logical reasoning ability (LRA), and thinking transformation ability (TCA). Consider self-control at the class level as the second-level variable. The research results show that the five cognitive abilities have a significant positive impact on comprehensive academic performance. Self-control plays an active role in regulating the relationship between RA, LRA, TCA, and comprehensive academic performance.