In order to explore the influence of the polymorphism in the 20 intron region of the Sansui duck ATP2A2 gene on the eggshell quality, this study used Primer Premier 5 software to design and synthesize a pair of primers in the 20 intron region, two-way direct sequencing and sequence alignment to mine SNPs Sites, SPSS 18.0 software was used to analyze the relationship between SNP sites and eggshell quality of Sansui duck. Results Three SNP sites were found in the 20 intron region of the ATP2A2 gene: g.40874 T>C, g.40920 G>A and g.40990 T=C, all of which were moderately polymorphic, at the site g.40874 T ＞C and g.40920 G＞A both deviated significantly from Hardy-Weinberg equilibrium (P>0.05), position g.40990 T=C accords with Hardy-Weinberg equilibrium (P<0.05), and position g.40874 T＞C There is a strong linkage disequilibrium between g.40990 T=C; a total of 4 haplotypes and 9 double types were detected at 3 SNP loci; the results of association analysis show that g.40874 T＞C mutation has an effect on eggshell strength The eggshell strength of CC genotype was significantly higher than that of TC and TT genotypes (P<0.05), and the eggshell weight of CC genotype was significantly higher than that of TC genotype (P<0.05), g. The 40990 T=C mutation has a significant effect on the eggshell strength, and the eggshell strength of the TC genotype is significantly higher than that of the TT genotype (P<0.05). In summary, the g.40874 T>C and g.40990 T=C found in the 20th intron region of the Sansui duck ATP2A2 gene may be the marker sites that affect the quality of the eggshell.