We propose a systematic method for the appropriate materials design for thermosetting resin based on computer simulations. The proposed method is a combination of the molecular dynamics (MD) simulation and self-organizing maps (SOMs). The MD simulation is alternative to experiments that consists the curing reaction and mechanical test of the epoxy resin. In particular, in order to obtain the natural cross-linked structure of the epoxy resin, we conducted curing simulation wherein the activation energy and heat of formation are considered for the chemical reaction. On the other hand, SOMs enables us to classify the materials species in accordance with the similarity in their characteristics. From the classification of the 25 species in the epoxy resins, we found that epoxy systems that have base resins with multi-functional groups express superior mechanical properties. Moreover, the molecular scale mechanism of the higher mechanical properties was hydrogen-bonding extended throughout the system.