Perfluoroalkyl carboxylic acids (PFCAs) are some of the most significant pollutants in human serum, and are reported to be potentially toxic to humans. In this study, the binding mechanism of PFCAs with different carbon lengths to human serum albumin (HSA) was studied at the molecular level by means of fluorescence spectroscopy under simulated physiological conditions and molecular modeling. Fluorescence data indicate that PFCAs with a longer carbon chain have a stronger fluorescence quenching ability. Perfluorobutanoic acid (PFBA) and perfluorohexanoic acid (PFHxA) had little effect on HSA. Fluorescence quenching of HSA by perfluorooctanoic acid (PFOA) and perfluorodecanoic acid (PFDA) was a static process that formed a PFCA-HSA complex. Electrostatic interactions were the main intermolecular forces between PFOA and HSA, while hydrogen bonding and van der Waals interactions played important roles in the combination of PFDA and HSA. In fact, the binding of PFDA to HSA was stronger than that of PFOA as supported by fluorescence quenching and molecular docking. In addition, infrared spectroscopy demonstrated that the binding of PFOA/PFDA resulted in a sharp decrease in the β-sheet and α-helix conformations of HSA. Our results indicated that the carbon chain length of PFCAs had a great impact on its binding affinity, and that PFCAs with longer carbon chains bound more strongly.