The study on bisphenol A epoxy resin (EP)/4,4'-Diaminodiphenylmethane (DDM) system modified with poly(aryl ether ketone) (PEK-C) by the method of melt blending process is reported. The microscopic phase structure and morphology of impact fractured surface were observed by SEM, the phenomenon of microscopic phase separation and heat resistance property were studied by DMA. The results showed that PEK-C can disperse in the blends in the form of nanometer size (<100nm) particles or in the form of molecular size when the content of PEK-C lower than 10%, and the nano-particles are uniformly dispersed in the blends. The rough region of impact fractured surface with PEK-C modified sample is larger and more obvious, which indicated that toughness of the blends has been improved. The modified system has microscopic phase separation characteristics with higher content of PEK-C, as the same observed result of SEM, the glass transition temperature (Tg) of the blends moves towards higher temperature with the increasing content of PEK-C and the property of heat resistance has been improved.