Objective This study was to investigate the characteristics of insulin secretion and the 25-hydroxyvitamin D3 (25(OH)D3) levels in children with obesity. Methods A retrospective analysis was conducted among children who underwent health checkups in the pediatric healthcare department of our hospital from January 2018 to January 2021, and they were divided into a normal group and an obese group according to their BMI. The insulin secretion and the 25(OH)D3 levels of the two groups of children were compared. A total of 721 children were included in the study, including 591 in the normal group and 130 in the obese group, with an obesity rate of 18.03%. Results The blood glucose of the normal group was 4.55 ± 1.75 mmol/L, and the 2 h PG was 7.51 ± 2.11 mmol/L; in the obesity group, they were 6.03 ± 2.16 mmol/L and 8.92 ± 3.24 mmol/L, respectively. The FPG and 2 h PG in the obese group were significantly higher than those in the normal group (all P < 0.05). The incidence of IFG/IGT in the normal group was 5.24% (31/591), and the incidence of DM was 3.71% (22/591); the incidence of IFG/IGT in the obese group was 14.62% (19/130), and the incidence of DM was 13.08% (17/130). The incidences of IFG/IGT and DM in the obese group were significantly higher than those in the normal group (P < 0.05). The FINS of the children in the normal group was 18.46 ± 3.15 μU/mL, and the HOMA-IR was 2.64 ± 0.62; the above indicators in the obese group were 19.11 ± 4.72 μU/mL and 3.01 ± 0.83, respectively. The FINS and HOMA-IR in the obese group were significantly higher than those in the normal group (P < 0.05). The serum 25(OH)D3 level in the normal group was 28.15 ± 5.27 ng/mL, of which 556 cases were normal in 25(OH)D3 and 35 cases were deficient in 25(OH)D3. The serum 25(OH)D3 level in the obese group was 24.35 ± 4.51 ng/mL, of which 112 cases were normal in 25(OH)D3 and 18 cases were deficient in 25(OH)D3. The level of serum 25(OH)D3 in the normal group was significantly higher than that in the normal group, and the ratio of 25(OH)D3 deficiency was significantly lower than that in the normal group (P < 0.05). Conclusions The blood glucose level of childhood obesity was significantly increased, the incidence of abnormal glucose metabolism and diabetes was significantly increased, and the level of 25(OH) vitamin D3 was significantly decreased. Lifestyle improvements and vitamin D supplementation play an important role in the prevention of childhood diabetes. Because the major causes of childhood obesity are excessive caloric intake and lack of exercise, the most effective and direct measures to prevent obesity are a reasonable lifestyle, reasonable eating habits, and moderate exercise. Although genetics are critical, there is no reliable way to eliminate obesity genes in the human body. Therefore, the role of obesity genes is required to be ultimately eliminated by reduced caloric intake and increased physical activity.