By incorporating 1-(2-aminoethyl)piperazine (AEPIP) into a commercial epoxy blend, a bicontinuous microstructure is produced with the selective localization of amine-functionalized graphene nanoplatelets (A-GNPs). This cured blend underwent self-assembly, and the morphology and topology were observed via spectral imaging techniques. As the selective localization of nanofillers in thermoset blends is rarely achieved, and the mechanism remains largely unknown, the optical photothermal infrared (O-PTIR) spectroscopy technique was employed to identify the compositions of microdomains. The A-GNP tends to be located in the region containing higher concentrations of both secondary amine and secondary alcohol; additionally, the phase morphology was found to be influenced by the amine concentration. With the addition of AEPIP, the size of the graphene domains becomes smaller and secondary phase separation is detected within the graphene domain evidenced by the chemical contrast shown in the high-resolution chemical map. The corresponding chemical mapping clearly shows that this phenomenon was mainly induced by the chemical contrast in related regions. The findings reported here provide new insight into a complicated, self-assembled nanofiller domain formed in a multicomponent epoxy blend, demonstrating the potential of O-PTIR as a powerful and useful approach for assessing the mechanism of selectively locating nanofillers in the phase structure of complex thermoset systems.