Both phloretin and phlorizin (phloretin 2′-O-glucoside) extracted from the peel of apples are attributed to particular flavonoid dihydrochalcones with multiple pharmacological activities. However, metabolite structural characterization of these two components, which may accumulate to exert their pharmacological effects, remains insufficient. The present study aimed to comparatively clarify the metabolic pathways of phloretin and phlorizin after oral administration individually to Sprague-Dawley (SD) rats. Therefore, a rapid, integrate and systematic analytical strategy based on characteristic fragment ion fishing was proposed for the screening and identification of metabolites coming from phloretin and phlorizin using UHPLC-Q-Exactive Orbitrap mass spectrometry in parallel reaction monitoring mode. As a result, a total of 50 phloretin metabolites and 52 phlorizin metabolites were individually identified from different biological samples including rat plasma, urine, and faeces. Moreover, glucuronidation, sulfation, carbonylation and hydrolyzation were revealed to be the main metabolic pathways of phlorizin, while decarbonylation, glucuronidation and sulfation were regarded as the predominant biotransformation pathways as for phloretin. This is the first systematic study on comparison of metabolic profiles of phlorizin and phloretin in disease states, which was helpful to declare the complicated structure activity relationships between phlorizin and phloretin and shed light to their action mechanism.