Logistic regression analysis indicated that female (OR 2.129, 95% CI 1.615–3.022), waist circumference ≥ 90 cm (OR 3.814, 95% CI 2.778 ~ 4.312), diabetes (OR 2.856, 95% CI 1.905 ~ 3.448), FG ≥ 88 mg/dL (OR 1.551, 95% CI 1.284 ~ 2.183), triglyceride ≥ 160 mg/dL (OR 1.804, 95% CI 1.236–2.845), HDL-C ≤ 0.8 mmol/L (OR 2.032, 95% CI 1.614–3.079), LDL-C ≥ 2.0 mmol/L (OR 1.926, 95% CI 1.442–2.041) and apolipoprotein B ≥ 0.70 g/L (OR 2.119, 95% CI 1.658–2.873) were the risk factors of obesity in patients with schizophrenia (all p < 0.05). The gene discussed is APOB; the disease is Obesity.