Demands for chemical-free treatments for controlling insect pests are increasing worldwide. One such treatment is microwave heating; however, two critical issues arise when using microwaves as a heat source: intensive labor and excessive energy-consumption. Optimization is thus required to reduce energy consumption while effectively killing insects. Currently, the lethal effect of microwaves on insects is considered to be due to the temperature of the irradiated materials. This study examines how the conditions of irradiation, such as resonance or traveling mode, changed the conversion of electromagnetic energy into heat when 2.45 GHz microwaves penetrated the body of the termite, C. formosanus. Our results indicated that it is possible to heat and kill termites with microwaves under resonance condition. Termites were however found to be very tolerant to microwave irradiation as the permittivity of the insect was low compared with other reported insects and plants. Electron spin resonance revealed that termites contained several paramagnetic substances in their bodies, such as Fe3+, Cu2+, Mn2+, and organic radicals. Interestingly, irradiation with traveling microwaves hardly produced heat, but increased the organic radicals in termite bodies indicating non-thermal effects of microwaves.