Objective To explore the relationship between physical fitness index and executive function in Chinese adolescents, and to provide a reference for improving the development of executive function in Chinese adolescents. Methods From September to December 2023, 5336 adolescents aged 13 to 18 years were selected by stratified whole cluster random sampling method in six regions of China for physical fitness and executive function tests. The relationship between adolescent physical fitness index and executive function was analyzed using t-test, ANOVA, Pearson’s correlation, and logistic regression. Results The correlation coefficients between adolescents’ physical fitness index and inhibitory control reaction time were all 0.00094, p > 0.05; the correlation coefficients between adolescents’ physical fitness index and working memory (1-back, 2-back) reaction time were −0.13 and −0.093, respectively, p < .05; the correlation coefficients between adolescents’ physical fitness index and cognitive flexibility reaction time were −0.17 and −0.18, p < .05. Logistic regression analyses showed that 1-back, 2-back, and cognitive flexibility were significantly and positively correlated with physical fitness index in Models 1, 2, and 3 (all p values less than.01). The coefficients of inhibitory control were not significant in all three models (p > .05), and there was no significant relationship with physical fitness index. Conclusion The physical fitness index of Chinese adolescents has a significant positive correlation with working memory and cognitive flexibility, but not with inhibitory control, i.e. the higher the physical fitness index, the better the working memory and cognitive flexibility.