This study examines the effect of cationic initiator structure on the curing behavior and thermal conductivity of epoxy systems. Naphthalene-modified initiators were designed to enhance molecular stability, and their curing behavior was tuned by varying the counter anions. Differential scanning calorimetry (DSC) revealed prolonged and controlled curing behavior compared to conventional cationic initiators, reflecting improved thermal stability of the initiator structures. The initiators were applied to both conventional and liquid crystalline epoxy systems to promote the formation of ordered polymer networks during curing. As a result, epoxy systems cured with these initiators exhibited improved thermal conductivity, attributed to enhance structural ordering enabled by stable and controlled curing. This work demonstrates that molecular design of cationic initiators is an effective approach for tuning curing behavior and thermal conductivity in epoxy systems.