Objective To investigate the distribution of homeostasis model assessment-insulin resistance (HOMA-IR) index and its relationship with metabolic syndrome and inflammatory cytokines in students aged 7 to 14 years. Methods The data of 366 students (n=163 for boys and n=203 for girls) aged 7 to 14 years were collected, including anthropometric parameters (height, body weight, body mass index, waist circumference, hip circumference and waist-hip ratio), blood pressure, total fat mass, fat proportion, fasting blood lipid, fasting blood glucose, fasting insulin and serum levels of inflammatory cytokines such as tumor necrosis factor-α (TNF-α), C-reactive protein (CRP) and interleukin-6 (IL-6), and insulin resistance was evaluated by HOMA-IR index. Results The 75th percentile of HOMA-IR index for boys and girls was 3.62 and 2.88, respectively. Body weight, height, body mass index, waist circumference, hip circumference, total fat mass and fat proportion were positively related to HOMA-IR index (P<0.01). When HOMA-IR index surpassed 75th percentile, age, anthropometric parameters, total fat mass, fat proportion and systolic blood pressure significantly increased in boy and girl students (P<0.05), no significant change occurred in diastolic blood pressure in boy and girl students, the levels of serum TNF-α and IL-6 significantly increased in boy students (P<0.05), while there was no significant change in level of CRP in boy students and levels of CRP, TNF-α and IL-6 in girl students. Conclusion The increase of HOMA-IR index leads to a dramatic increase of anthropometric parameters, total fat mass, fat proportion and serum TNF-α and IL-6 in boy students, while that results in the increase of anthropometric parameters, total fat mass and fat proportion in girl students, with no significant change in serum inflammatory cytokines.