In view of the low toughness of high temperature epoxy resin, phenolphthalein-based polyaryletherketone (PEK-C) was adopted to toughen and modify high temperature epoxy resin. The effects of the molecular weight and content of PEK-C on the curing reaction, toughening effect and heat resistance of the modified resin were studied. The results show that the addition of PEK-C has little effect on the curing reaction and heat resistance, but it can significantly improve the toughness of the epoxy resin. The 15% PEK-C with the molecular weight of 8×104 modified resin has the best mechanical properties, the tensile strength and elongation at break reach 80 MPa and 3.1%, respectively, which are 68% and 121% higher than those of the unmodified resin, respectively. The impact toughness is ss high as 23.3 kJ/m2, which is 99% higher than that of the unmodified resin. The microphase structures of the modified resins with different PEK-C contents were characterized by transmission electron microscopy (TEM). With the increase of PEK-C content, the phase structure transition from sea-island phase to bicontinuous phase inversion was sequentially observed.