The fluorinated surfactant sodium perfluorooctanoate (SPFO) could bind onto ubiquitin (UBQ) and induce the unfolding of UBQ. By using (15)N-edited heteronuclear single-quantum coherence (HSQC) NMR and (19)F NMR to monitor (15)N-labeled UBQ and SPFO, respectively, the binding sites and the aggregation process of SPFO on UBQ at various SPFO concentrations were observed. A detailed process from specific binding to cooperative binding of SPFO on UBQ, and a detailed structure change of UBQ upon the increase of SPFO concentration were obtained. The refolding of UBQ in UBQ-SPFO complex was carried out by adding cationic surfactant. It was shown that added cationic surfactants formed mixed micelles with SPFO and resulted in the dissociation of the UBQ-SPFO complex, and consequently, most ubiquitin could be refolded to its native state.