Systemic acquired resistance (SAR) is a plant defense response that provides long-lasting, broad-spectrum pathogen resistance to uninfected distal leaves following an initial localized infection. However, little information is available on the molecular biological basis of SAR especially in uninfected distal leaves. Here, we used two SAR-induced bacteria to induce SAR in Arabidopsis, a metabolomics approach based on ultra-high-performance liquid chromatography (UPLC) and mass spectrometry (MS) technique was used to identify SAR-related metabolites in SAR-induced bacteria infected local leaves and distal leaves of locally SAR-induced bacteria infected plants. Multiple statistical analyses were used to identify differentially expressed metabolites (DEMs). The result showed primary metabolism and secondary metabolism were significantly altered in local leaves and distal leaves, including phenolic compounds, amino acids, nucleotides, organic acids and many other metabolites. Furthermore, the content of amino acids, phenolic compounds, coenzymes and its derivatives increased in distal leaves, suggesting these metabolites contributed to the establishment of SAR. In addition, 2’-hydroxy-4,4’,6’-trimethoxychalcone, phenylalanine and ethyl docosahexaenoate were identified as potential components which may play important role both in basic resistance and SAR. This study provided a reference for understanding metabolic mechanism associated with SAR in Arabidopsis, which will be useful for further investigation of the molecular basis of SAR.