Agricultural application contributes major consumption of antibiotics worldwide. As veterinary antibiotics are poorly metabolized by animals, most of them end up in agricultural waste, which is increasingly subject to thermal treatment, such as torrefaction, pyrolysis, etc. However, there is a lack of research on their thermal decomposition mechanisms and products elucidation. Therefore, this study investigated the thermal decomposition of four major veterinary antibiotics groups (β-lactams, tetracyclines, fluoroquinolones, sulfonamides) with emphasis on their thermal stability, structural transformation and antibacterial activity. Results show that thermal treatment can remove the parent antibiotics with their antibacterial activity except for gatifloxacin (GAT). Although the parent form of GAT was fully removed at 200 °C, its products showed significant antibacterial activity against E. coli. We present novel evidence that the PhO-CH3 chemical bond on GAT preferentially brake to generate methyl radical, which underwent a substitution reaction at the para position of phenol. This reaction also occurred during the thermal decomposition of antibiotic analogues, balofloxacin and moxifloxacin, whose thermolysis products also showed significant antibacterial activity. Furthermore, these thermolysis products may present potentially cardiotoxic and pose higher risks to human health than their parent forms, based on the comparison with a group of drugs withdrawn from the market.