To determine the effects of microwave radiation at the molecular level as well as on the germination, growth and morphology of dry spores at the single-cell level. Dry Bacillus aryabhattai MCCC 1K02966 spores were microwave-treated at different powers and characterized using single-cell optical technology. As determined by laser tweezers Raman spectroscopy, the Ca${}^{2+}$-dipicolinic acid content increased and nucleic acid denaturation occurred in response to microwave treatment. Live-cell microscopy revealed that the germination and growth rates decreased as the microwave power increased. With respect to morphology, atomic force microscopy (AFM) demonstrated that spores became wrinkled and rough after microwave treatment. Furthermore, spores became smaller as the microwave power increased. Microwave treatment can damage DNA, and high-power microwaves can inhibit the germination of spores and reduce spore volumes. These results provide a new perspective on the responses of living single cells to microwave radiation and demonstrate the application of various new techniques for analyses of microorganisms at the single-cell level.To determine the effects of microwave radiation at the molecular level as well as on the germination, growth and morphology of dry spores at the single-cell level. Dry Bacillus aryabhattai MCCC 1K02966 spores were microwave-treated at different powers and characterized using single-cell optical technology. As determined by laser tweezers Raman spectroscopy, the Ca${}^{2+}$-dipicolinic acid content increased and nucleic acid denaturation occurred in response to microwave treatment. Live-cell microscopy revealed that the germination and growth rates decreased as the microwave power increased. With respect to morphology, atomic force microscopy (AFM) demonstrated that spores became wrinkled and rough after microwave treatment. Furthermore, spores became smaller as the microwave power increased. Microwave treatment can damage DNA, and high-power microwaves can inhibit the germination of spores and reduce spore volumes. These results provide a new perspective on the responses of living single cells to microwave radiation and demonstrate the application of various new techniques for analyses of microorganisms at the single-cell level.