To investigate the regulation mechanism of TAP1 gene methylation modification on the resistance to E.coli F18, Bisulfite sequencing PCR (BSP) + Miseq was used to analyze TAP1 gene promoter methylation level in duodenum and jejunum tissues from Sutai E. coli F18-resistant and sensitive weaning piglets, and mRNA expression of TAP1 gene was detected by real-time PCR (qRT-PCR), then analyzed the associations between the methylation level of TAP1 gene promoter and mRNA expression. The results showed that in TAP1 gene promoter region there were 28 CpG sites between the two CpG islands and middle non-CpGarea, and all the sites were in different degrees of methylation. At the CpG-6 site, the methylation level of resistant group in jejunum tissue was significantly lower than that of the sensitive group (P<0.05).At the CpG-7 and CpG-8 site, the methylation level of resistant group in duodenum tissue was significantly higher than that of the sensitive group (P<0.05).The methylation level of CpG-7 and CpG-8 site was negatively correlated with TAP1mRNA expression. Thus, we speculated that CpG-6, CpG-7 and CpG-8 may be the key sites for regulating gene transcription, and the weaning piglets could improve the mRNA expression through the methylation level in the duodenum and jejunum tissue to regulate E. coli F18 resistance.