We analysed the metabolic rate of large individuals (LIs) and small individuals (SIs) (based on body weight) of 80-day-old specimens of Portunus trituberculatus injected with 40 mg/kg florfenicol (FLR). The results showed that FLR contents in the gills and hepatopancreas were higher in the SIs than in the LIs. The activities of erythromycin N-demethylase and 7-ethoxyresorufin-O-deethylase related to cytochrome oxidase P450 (CYP) were induced after FLR injection and showed a size-dependent pattern; however, no significant difference in aminopyrine N-demethylase activity was found between the LIs and SIs. The activity of the phase II enzyme glutathione S-transferase (GST) increased in the hepatopancreas after FLR injection, and it was higher in the SIs than the LIs. Moreover, induction of CYP2, CYP3, GST, ABCB and ABCG was observed in the first 24 hr after FLR injection. FLR caused more biomolecular damage in the SIs than the LIs, displaying an obvious body weight- and time-dependent pattern. In summary, the SIs exhibited faster FLR uptake and slower depuration in this species, and FLR caused more biomolecular damage to the SIs.