Objective: To determine the relationship between body mass index (BMI) and physical fitness index (PFI) in Chinese and Japanese children and adolescents and to provide theoretical support for physical fitness improvement in Chinese children and adolescents. Methods: A total of 9 594 children and adolescents aged 7-18 years were tested in China and Japan, 4 800 of which with various BMI were randomly selected for analyzing and comparing PFI between the two countries. The relationship between different BMI-Z scores and PFI was analyzed. Results: In general, the PFI of wasting, normal weight, overweight and obesity in Chinese boys was -1.17, -0.03, 0.04 and 0.26, the figures were -2.59, -0.34, -1.46 and -2.44 for Japanese boys, significant differences were found in overweight and obese group (P<0.01). the PFI of wasting, normal weight, overweight and obesity in Chinese girls was -1.18, -0.08, 0.01 and 1.03, the figures were -1.21, 0.51, 0.11 and -1.30 for Japanese girls, significant differences were found in normal weight and obese group(P<0.05). Significant differences in PFI were found within Chinese boys, Chinese children, Japanese boys, Japanese girls and Japanese children with different BMI-Z levels(F=2.89, 3.05, 4.81, 2.33,5.34,P<0.01). Conclusion There is an inverted "U" curve relationship between BMI and PFI in Chinese and Japanese children and adolescents. With the increase of BMI-Z score, decreasing rate of PFI in Chinese boys is higher than Japanese boys. Practical and effective intervention measures should be taken to improve physical fitness of children and adolescents in China.