Childhood obesity can lead to adulthood obesity with adverse effects. Since body composition and physical fitness differ depending on the obesity degree, a systemic analysis could help classify that degree. We used three study designs based on the obesity degree (body mass index [BMI] as a reference) for our objectives. First, we identified the relationship between body composition and physical fitness. Second, we determined the effects of exercise on body composition and physical fitness. Third, we performed a path analysis of the impact of exercise on body composition and physical fitness, and verified those effects among the groups. In study 1, 164 10-year-old subjects were divided into four groups: 33 in the normal weight (NO), 34 in overweight (OV), 54 in obesity (OB), and 43 in the severe obesity (SOB) group. In study 2, 101 participants from study 1 who wished to participate in the exercise program were divided into four groups (same criteria). The exercise program (three times a week for 60 min, for 16 weeks) consisted of sports and reinforcement exercises of increasing intensity. Body composition was measured by body weight, percentage of body fat (%BF), muscle mass, skeletal muscle mass (SMM), and body mass index (BMI). In contrast, physical fitness was measured by muscular strength, flexibility, muscular endurance, agility, and balance. As a result, all body composition variables were higher in the SOB group than in the other groups. Physical fitness, muscular strength and balance, and agility were highest in the SOB, NO, and OV groups, respectively. Pearson’s correlation revealed that muscular strength was associated with height and body weight across all groups. Agility showed a negative correlation with %BF in the NO, OB, and SOB groups. SMM was positively correlated in the OB and SOB groups. After the exercise intervention, BMI and the %BF of the SOB group were significantly reduced (p < 0.01, and p < 0.001, respectively), while SMM presented a significant increase (p < 0.001). Height also showed a significant increase in all groups (p < 0.001). Among physical fitness variables, muscular strength, flexibility, muscular endurance, and balance showed a significant increase in all groups, while a significant increase in power was observed in only the OB and SOB groups. As for the effects of the body composition on physical fitness after exercise intervention, the greatest impact was observed for balance, muscular strength and agility, and muscular endurance in NO, OV, and OB groups, respectively. In conclusion, the body composition, physical fitness relationship, and the effects of exercise intervention on them differed depending on the obesity degree. Furthermore, the results varied according to the obesity degree. Thus, our study highlights the importance of creating particular exercise programs for the effective prevention and treatment of childhood obesity considering the obesity degree.