CREB-regulated transcription coactivator 3 (CRTC3) was a recently identified protein which played an important role in glucose and lipid metabolism. Previous research showed that the polymorphisms of CRTC3 were associated with obesity in Mexican-Americans. Data on that relationship in Chinese was unavailable so far. So we investigated whether the polymorphisms of CRTC3 could confer risks of obesity or other metabolic disorders in Chinese population. 1,550 subjects were recruited from physical examination participants. Two SNPs of CRTC3, rs3862434 and rs11635252, were genotyped with the method of PCR-RFLP. Logistic regression model was applied to calculate the risks of overweight, obesity and dyslipidemias for genotypes. The rs3862434 was significantly associated with the plasma level of total cholesterol (P = 0.026), with the G allele carriers having a lower level compared with the AA genotype (P = 0.018). The rs11635252 was associated with the risks of overweight and hypertriglyceridemia, specifically, T allele had higher risks of overweight and hypertriglyceridemia compared with C allele (OR 1.23, 95 % CI 1.02-1.48, P = 0.024; OR 1.22, 95 % CI 1.00-1.48, P = 0.048, respectively). In conclusion, the CRTC3 polymorphism rs3862434 was associated with the plasma level of total cholesterol, and rs11635252 was associated with the risks of overweight and hypertriglyceridemia in a Chinese Han population, which might strengthen our understanding of the complex heredity of metabolic disorders.