Objective To investigate the effect of electromagnetic pulse (EMP) on the the link-structure of heart intercalated discs(ID), and to explore the mechanism involved. Methods EMP was provided by the EMP simulator of our department, the parameters was as following: 200 pulse, different field intensity(50～400 kV/m). The research objects were female SD rats, they were randomly divided into five groups, each group has six rats. At 12 h after EMP exposure, the lanthanum nitrate tracer method and the transmission electron microscope (TEM) were used to observe the structural changes of left ventricular myocardium. Microarray was used to evaluate the gene differential expression of left ventricular myocardium. Results At 12 h after EMP exposure, the width of ID gap was widen gradually with field augmentation, lanthanum nitrate in ID gap was incrsased gradually with field augmentation. Compared with the control group, there were 108 genes standard altered in gene expression profile in rat myecardium after EMP in the 200 kV/m group. 51 genes (synaptorin, VGF, HSP70, etc.) were up-regulated while 57 genes (NAD, FGF, Tff3, etc.) were down-regulated. Conclusions Space between intercalated discs was wided along with field augmentation after EMP exposureed. The changes in ID of cardiac muscle was remarkable at 400 kV/m. There were 108 genes altered in gene expression profile in rat myocardium after EMP.