Background: Nuclear factor erythroid 2-related factor 2 (Nrf2, also called NFE2L2) has been shown to play a pivotal role in preventing cancer cells from being affected by chemotherapy. Gene mutation is a crucial reason of chemotherapy-resistance in acute myeloid leukemia (AML). However, the relationship between Nrf2 and tumor mutation burden and its mechanism in regulating chemotherapy-resistance remains unclear. Methods: The whole-exome sequencing analysis were used to measure tumor mutation. RNA sequencing, Oncomine, qRT-PCR, Western blotting and immunocytochemistry were employed to detect differences in genes and proteins. The KEGG pathway enrichment analysis and GeneMANIN were performed pathway analysis. Functional assays, such as annexin V/PI, Hoechst33342 staining and DCFH were performed to examine the apoptosis and reactive oxygen species (ROS) of AML cells in vitro. Subcutaneous xenograft model was established to investigate in vivo growth. Results: Nrf2 expression was associated with tumor mutation burden in AML. Patients with Nrf2 overexpression had higher frequency of gene mutation and drug resistance. Nrf2 overexpression protected the AML cells from apoptosis induced by cytarabine in vitro and increased the risk of gene mutant drug resistance in vivo. Furthermore, Nrf2 overexpression inhibited MSH2 protein expression, which caused DNA mismatch repair (MMR) deficiency. Mechanistically, the inhibition of MSH2 by Nrf2 was in a ROS-independent manner. Further studies showed that an increased activation of JNK/c-Jun signaling in Nrf2 overexpression cells, which inhibited the expression of MSH2 protein. Conclusions: Our findings provided evidence that high Nrf2 expression inhibited MSH2 expression, caused MMR deficiency and increased the tumor mutation burden, which can induce gene instability-dependent drug resistance in AML. This study demonstrates the reason why the high Nrf2 expression leads to the increase of gene mutation frequency in AML, and provides a new strategy for clinical practice.