In this study, the high-throughput Illumina HiSeq 2000 mRNA sequencing technique was used to investigate the transcriptome response of Escherichia coli O157:H7 exposed to ohmic heating (OH) and water bath heating (WB). Compared to untreated samples, a total of 293, 516, and 498 genes showed differential expression after HVOH (high voltage short time ohmic heating), LVOH (low voltage long time ohmic heating), and WB, respectively. Therefore, LVOH had the potential to cause comparable effects on the transcriptome of E. coli O157:H7 as compared to WB, but not HVOH. These results indicated that additional non-thermal effects were not reflected on transcriptome of E. coli O157:H7 using both HVOH and LVOH, in particular the HVOH. Most of differentially expressed genes involved in information storage and processing, and cellular processes and signaling showed up-regulation whereas most of genes related to the metabolism were down-regulated after HVOH, LVOH, and WB. In addition, more attention needs to be paid to the up-regulation of a large number of virulence genes, which might increase the ability of surviving E. coli O157:H7 to infect host cells after HVOH, LVOH, and WB. This transcriptomic study on the response of E. coli O157:H7 to OH protomes the understanding of inactivation mechanism of OH on the molecular level and opens the door to future studies for OH.