A heterogeneous molecular network of trifunctional epoxy resins was designed by using a two-step polymerization strategy to improve the toughness and thermal properties without sacrificing the modulus and strength. In this strategy, epoxy resin was premixed with an ionic liquid (IL) and then the prereacted epoxy-IL was dispersed into epoxy with curing agent to finish the curing. It was found that the fracture toughness of the designed epoxy resin was significantly improved by 117% in comparison with that of the neat epoxy. Meanwhile, 45.9% and 74.8% increases in the tensile strength and elongation at break were obtained, respectively. Moreover, thermal stability and heat resistance of the designed epoxy resin were also enhanced. It is suggested that some highly cross-linked and more complete epoxy-IL networks were formed during the two-step reaction process, which can deflect the cracking path and restrict the molecular mobility of the network at high temperatures.