The binding mechanism between pefloxacin mesylate (PM) and transferrin (Tf) was explored using spectral experiment combined with molecular modeling techniques.  The binding parameters and  thermodynamic functions of PM-Tf solution system were measured at different temperatures.  The effect of M on molecular conformation of Tf was investigated and the interaction mechanism was also discussed.  The results showed that dynamic quenching mechanism occurs with PM binding to Tf.  The value of binding distances (r) is low, which indicates the occurrence of energy transfer.  The drug had conformational effect on Tf, which resulted in changes of hydrophobic environment of the binding domain in Tf.  According to the obtained thermodynamic parameters, the main interaction force between PM and Tf is attributed to hydrophobic bonding.  The results of molecular modeling revealed that hydrophobic and hydrogen bonds are main binding forces in the PM-Tf system.  These results were in accordance with spectral experiments.  The research results have given a better theoretical reference for the study of pharmacological mechanism between protein and quinolone.