Fleroxacin (FLRX) is a new member of the class of fluoroquinolones, its effects on human serum albumin (HSA) and the mechanism of action are poorly understood, Especially, the secondary structural alterations of HSA induced by FLRX and the inner filter effect, which resulted in a spurious decrease in the observed fluorescence intensity and affected the binding parameters calculated from it are not considered. In this paper, binding of FLRX to HSA has been studied using multi-spectroscopy and molecular modeling methods. Fluorescence spectra revealed that the observed fluorescence quenching of HSA by FLRX was due to a 1∶1 complex formation by a static quenching process with a constant of 105 L·mol-1. The thermodynamic parameters (ΔH and ΔS) were calculated to be -107.99 kJ·mol-1 and -240.99 J·mol-1·K-1 via the Van’t Hoff equation, which indicated that hydrogen bond and van der Waals force were the dominant intermolecular force. From the synchronous fluorescence, FT-IR and three dimensional fluorescence spectra, it was evident that the binding of FLRX to HSA induced a conformational change in the protein, and the alterations of secondary structure were quantitatively calculated by the evidence from FTIR spectra with reductions of α-helices of about 18.3%, decreases of β-sheet structures of about 9.6%, and increases of β-turn structures of about 18.0%. Site marker competitive experiments showed that phenylbutazone and FLRX shared a common binding site Ⅰ corresponding to the subdomain Ⅱ A of HSA. The binding details between FLRX and HSA were further confirmed by molecular docking studies, which revealed that FLRX was bound at subdomain Ⅱ A through multiple interactions, such as hydrogen bond, hydrophobic and van der Waals, etc. The accurate and full basic data in the work is beneficial to clarify the binding mechanism of FLRX with HSA and is helpful for understanding its effect on protein function during the blood transportation process.