Objective: To investigate the associations of reallocating sedentary time to different activity behaviors with body composition, and to provide a reference for prevention and control of childhood obesity. Methods: By using cluster random sampling, 1 621 students from 5 urban primary school in Guangzhou were selected in 2017. Vigorous intensity physical activity (VPA), moderate intensity physical activity (MPA), walking, sedentary behavior, and sleeping were measured by self-reported questionnaire. Inbody 230 was used to assess body composition. Multiple linear regression models were applied to examine isotemporal substitution effect of activity behaviors. Results: In younger children group (aged 6-9 years), replacing 30 min/day sedentary with VPA was associated with a 0.9% lower fat-free mass index(FFMI)(β=0.11, P=0.00). In older children group (aged 10-12 years), replacing 30 min/day sedentary with VPA was associated with a 1.0% lower FFMI(β=0.13, P=0.04); replacing 30 min/day sedentary to walking was associated with both a 2.9% lower percentage of body fat(PBF)(β=-0.65, P<0.01) and a 4.0% lower fat mass index(FMI)(β=-0.18, P=0.00). Conclusion Replacing sedentary with other intensities of physical activity is crucial for improving fatness status among children aged 6 to 12 years, especially among children aged 10 to 12 years. This current study suggests that children should increase physical activity while reducing sedentary for reducing risk of childhood obesity.