Abstract: The aim is to study the effect of the third intron in Arabidopsis pumila’s NPR1 gene on gene expression. Arabidopsis pumila NPR1 gene was cloned with the third intron, plant expression vector of NPR1 gene was constructed and Arabidopsis thaliana were transformed via Agrobacterium tumefaciens. After being induced 12 h with 5 mmol/L exogenous salicylic acid, the expression of the pathogenesis-related protein was detected with Real-time PCR. The results showed that the expression of NPR1, PR-1, PR-2, PR-5 in wild-type Arabidopsis thaliana was higher than those of the transgenic Arabidopsis thaliana. Compared with wild-type Arabidopsis thaliana, the SOD and POD activities significantly decreased in transgenic Arabidopsis thaliana, while the CAT activity did not increase significantly. The results showed that when the gene Ap.NPR1 containing the third intron was transferred into Arabidopsis thaliana, the transgenic plants systemic acquired resistance pathway was inhibited, and the plant disease resistance was reduced, which indicated that the third intron inhibited the gene expression of the systemic acquired resistance pathway.