Aim To investigate the relationship between single nucleotide polymorphism (SNP) of GATA6 gene promoter region－493 (rs144923558) G/A and －172 (rs146748749) G/A 2 sites and acute myocardial infarction (AMI) and their associated risk factors. Methods A case-control study was performed to collect 328 AMI patients and 344 normal controls (NC). Data were analyzed by polymerase chain reaction-restriction fragment length polymorphism technique combined with sequence alignment after DNA sequencing. After the Hardy-Weinberg balance test, the χ² test was used for correlation analysis; Logistic regression was used to analyze the relationship between multiple risk factors and two SNP loci and AMI incidence; linkage disequilibrium and haploid analysis was performed using Haplovview 4.2 software and SHEsis website. Results Three genotypes were detected in the two SNP loci, including GG, GA and AA. The genotype distribution was consistent with Hardy-Weinberg equilibrium (P>0.05), and there was no significant difference between the AMI group and the NC group(P>0.05). Multivariate Logistic regression analysis:age, hypertension, smoking, LDLC and TG were independent risk factors for AMI (P<0.05), and HDLC was protective factors (P<0.05) .Logistic regression analysis in three different genetic models of dominant, recessive and additive suggests that the two SNP loci are not associated with the onset of AMI. Linkage disequilibrium and haplotype analysis indicated that the two SNP loci were in the same linkage disequilibrium region (D′=1.000, r²=1.000), and haplotypes GG and AA did not increase AMI susceptibility (P>0.05). Conclusions The GATA6 gene promoter－493 (rs144923558) G/A and －172 (rs146748749) G/A two SNPs are completely unbalanced, of which GG is the main haplotype. The two SNP loci and their haplotypes were not associated with the onset of AMI, but provided population genetics of the GATA6 gene promoter region polymorphism.