This study evaluates the effect of gamma radiation on the spore activity, toxicity, and crystal structures of two engineered Bacillus thuringiensis (Bt) strains, TnX and TnY, and the reference Bt strain HD-1. We attempted to identify dosages of cobalt-60 gamma radiation that would inactivate Bt spores but not affect its toxicity. In the radiation dosage range of 10–15 kilogray, no viable spore formation and no significant reduction of the efficiency of Bt against lepidopteran larvae were observed. However, further sodium dodecyl sulfate Polyacrylamide gel electrophoresis (SDS-PAGE) results show that the components of the protoxin are affected by gamma radiation and that some bands are absent after treatment compared with the controls; the change in the protoxin band pattern depends on the type of Bt strain. Furthermore, the spore crystal structure of three Bt strains was studied with scanning electron microscopy and transmission electron microscopy. The results show that there are no changes in the size or shape of the treated Bt spores and crystals compared with the controls. The use of gamma radiation is effective to inactivate the spores of engineered Bt strains while preserving stable Bt toxicity against the target insect larvae.