Alcohol use disorder (AUD) has become a very serious medical and social problem. It is found that genetic polymorphisms of the 5-hydroxytryptamine receptors (5-HTRs) genes were associated with the risk of AUD. However, the results are controversial among different ethnic groups. At present, the correlation between 5-HTRs gene polymorphism and AUD in Han population from Yunnan Province remains unclear. In this study, 13 single nucleotide polymorphisms (SNPs) of HTR1B, HTR2A, HTR3A, HTR3B and HTR7 were detected by universal fluorescent probe technique. The CT genotype frequency of HTR3A rs1062613 was significantly higher in AUD case group than that in control group (P = 0.037, OR = 2.193, 95% CI: 1.048-4.366). The study indicated that the genetic polymorphisms of 5-HTRs were significantly associated with risk of AUD in Han male from Yunnan, China. In addition, this study further demonstrated the impact of alcohol on human health, especially liver damage, by analyzing the blood biochemical indicators of patients with AUD and combining them with their medical history.