Annonaceous acetogenins (Annona squamosa Linnaeus) comprises of a series of natural products which are extracted from Annonaceae species, squamocin proved to be highly efficient among those agents. Squamocin is mostly referred as a lethal agent for midgut cells of different insects, with toxic effects when tested against larva of some insects. In present study, LC50 and LC90 of squamocin for A. gemmatalis Hübner (Lepidoptera: Noctuidae) were calculated using probit analysis. Morphological changes in midgut cells were analyzed under light, fluorescence and transmission electron microscopes when larvae were treated with LC50 and LC90 of squamocin for 24, 48 and 72 h. Results revealed that the maximum damage to midgut cells was found under LC90 where it showed digestive cells with enlarged basal labyrinth, highly vacuolated cytoplasm, damaged apical surface, cell protrusions to the gut lumen, autophagy and cell death. The midgut goblet cells showed a strong disorganization of their microvilli. Likewise, in insects treated with squamocin, mitochondria were not marked with Mitotracker fluorescent probe, suggesting some molecular damage in these organelles, which was reinforced by decrease in the respiration rate in these insects. These results demonstrate that squamocin has potential to induce enough morphological changes in midgut through epithelial cell damage in A. gemmatalis.