Objective: To analysis the relationship between obesity types and exercise capacity among Mongolian primary school students, to provide evidence supporting the formulation of strategies to promote students physical fitness. Methods: A total of 7 941 Mongolian students aged 7-12 years in the Inner Mongolia Autonomous Region were selected, and data were collected from a field survey conducted by the National Physical Fitness and Health Survey in 2019. According to overweight and obesity screening of school aged children and adolescents, and the waist height ratio, obesity status was classified into general obesity, central obesity and complex obesity, relationships among obesity type, exercise ability and PFI. Results: The prevalence of obesity was 23.5%, 28.2%, 16.3% and 16.5% in boys and girls 7-9 and 10-12 years of age, respectively. The prevalence of obesity was higher in boys than girls( P <0.05). The detection rate of compound obesity in boys and girls was highest (15.6%, 9.2%; 18.4%, 8.2%), and the detection rate of compound obesity and central obesity in boys was higher than that in girls( P <0.05). The performance in the non obese boys and girls (on the basis of standing long jump, sit up and 50 m×8 round trip running in boys, and 50 m running, standing long jump, sit up and 50 m×8 round trip running in girls) was better than that in the obese groups( P <0.05). There were statistically significant differences in the median PFI of non obesity, general obesity, central obesity and compound obesity between boys and girls in the two groups of 7-9 and 10-12 years old (boys: H =79.23, 241.42; girls: H =61.94, 74.38, P <0.01). Conclusion The proportion of compound obesity among Inner Mongolian primary school students was relatively high, and the exercise capacity was relatively low. Specific measures should be taken to effectively control the occurrence and development of adolescent obesity.