Polyfluoroalkyl phosphates esters (PAPs) are widely used in a variety of commercial products, and have been detected in many aquatic organisms. In this study, common carps (Cyprinus carpio) were administered with 6:2 and 8:2 diPAP in water to investigate their bio-accumulation and transformation in fish. Several degradation products, including fluorotelomer unsaturated carboxylic acids (6:2 and 8:2 FTUCA), 5:3 and 7:3 fluorotelomer carboxylic acids (5:3 and 7:3 FTCA), perfluoroalkyl carboxylates (PFCAs) were identified in the carp liver. In addition, several phase-II metabolites, such as glutathione- and glucuronide-conjugated compounds were detected in the carp bile. 8:2 diPAP displayed lower accumulation potential than 6:2 diPAP probably due to its relatively large molecular size. However, 8:2 diPAP experienced more extensive transformation (transformation rate 6.78–14.6 mol%) and produced more phase I metabolites than 6:2 diPAP (0.49–0.66 mol%). The in vitro incubation with the liver S9 fraction confirmed that biotransformation of 6:2 and 8:2 diPAP took place in the carp liver. Further analyses of enzyme activities indicated that acid phosphatase (ACP) could be involved in mediating phase I while glutathione S-transferase (GST) involved in phase II metabolism of 6:2 and 8:2 diPAP in carp.