In this study, transcriptome analysis was conducted on the microarray data sets of peripheral blood collected from patients with ischemic cardiomyopathy and controls. The analysis was carried out in two phases. In phase 1, by comparing three sets of ischemic cardiomyopathy samples versus healthy controls, we identified three key genes—fibroblast growth factor binding protein 2 (FGFBP2), glucose-fructose oxidoreductase domain containing 1 (GFOD1), and megalencephalic leukoencephalopathy with subcortical cysts 1 (MLC1). These were considered as the potential mRNA biomarkers candidates. In phase 2, two gene expression data sets were collected on three points in time (the day of attack, 4-6 days of recovery, and 6 months of recovery). Differential analysis of gene pathways revealed that the seizure and recovery group were involved in the inflammatory and immune pathways compared with the control group. The seizure and recovery group (4-6 days) were involvedin the metabolic pathways or nerve secretion compared with the 6 months of recovery group. The experimental results show that the three potential mRNA biomarkers (FGFBP2, GFOD1 and MLC1) can be involved different pathways of ischemic cardiomyopathy, exhibiting continuous changes in the biological process.