With respect to rs1800849 of UCP3, the genotype of AA (AA vs GG, p = 0.026; ORAA vs GG = 1.75) was found to be a significant risk factor for prediabetes and after adjustment for age, sex, regular exercise, smoking, excessive drinking, hypertension and overweight, AA was still associated with an increased risk of prediabetes (aORAA vs GG = 1.68, 95% CI: 1.02–2.78); The recessive model also revealed a detrimental effect of AA for prediabetes (ORAA vs GA + GG = 1.72, 95% CI: 1.07–2.76; aOR AA vs GA + GG = 1.64, 95% CI: 1.02–2.66). Here, UCP3 is linked to prediabetes syndrome.