To evaluate the effect of 16 weeks of different aerobic activity on physical fitness and executive functions in primary school students. 90 right-handed students from China (Boys = 46; Girls = 44) participated in our study and were randomly separated into four groups: 20 in the control group (Con), 23 in the physical activity group (PA), 25 in the intellectual activity group (IA), 22 in the physical activity and intellectual activity group (PA + IA). The students in PA, IA and PA + IA group received aerobic exercise program lasted 40 min daily, 4 days a week for 16 weeks, regular physical activity in the PA group, intellectual activity in the IA group, physical activity couple with intellectual activity in the PA + IA group, respectively. All the students participate the experiment for body composition, physical fitness (cardiopulmonary fitness, muscle strength, speed sensitivity, flexibility quality), executive functions and saliva analysis test before and after 16 weeks. There was no significant effect of 16 weeks different aerobic exercise interventions on body composition before and after exercise interventions among four groups in children (p > 0.05). The results were obtained by inter-group and intra-group comparisons that different exercise interventions (physical activity, intellectual activity, physical combine with intellectual activity), all can significantly improve physical fitness parameters (cardiopulmonary fitness, muscle strength, speed sensitivity and flexibility quality), and executive functions parameters (inhibitory control, working memory, reaction time cognitive flexibility), as well as the concentration of saliva GH and IGF-I (p < 0.05) in children. Our experiment further demonstrated that the improvement effect of the two exercises together is more significant than that of the single exercise ways. Both physical and intellectual activity can effectively improve physical fitness and executive function in children, and the improvement effect of the two exercises together is more significant than that of the single exercise ways.