Foods of animal origin, as nutritional supplements, are usually consumed after cooking, but residues of amphenicols in fresh raw meat threaten human health. Therefore, this study was designed to evaluate the effects of boiling, deep-frying and microwave processing under different time conditions on the residue levels of amphenicols and metabolites in livestock and poultry meat. Antibiotic-free pork, beef, lamb and chicken samples were spiked with chloramphenicol (CAP), thiamphenicol (TAP), florfenicol (FF) and florfenicol amine (FFA) standard solutions and made into homogeneous meat blocks. These positive mock meat blocks were processed using three different cooking methods, and the analyses were performed by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The results showed that cooking methods, time and food matrices were the main factors influencing the changes in amphenicols and metabolites residues in livestock and poultry meat. With the increase in cooking time, boiling processing was the most effective in reducing the four drug residues in livestock and poultry meat matrices, followed by deep-frying, while microwaving caused an increase in drug residue concentrations. Although boiling and frying processes are effective strategies to reduce amphenicols and metabolites residues in meat, it cannot be assumed that these residues can always decrease to levels that are safe for consumer health, especially when the drug residue concentrations in raw meat are above the maximum residue limits (MRLs). Therefore, it is not reliable to remove residues of amphenicols and metabolites from food by cooking. The solution to the food safety problem of veterinary drug residues must start from the breeding source and accelerate the implementation of antibiotic reduction, antibiotic substitution and antibiotic-free farming.