The aggregation of multi-walled carbon nanotubes (MWCNTs) in the aqueous phase not only inhibits their extensive utilization in various aspects but also dominates their environmental fate and transport. The role of surfactants at low concentration in the aggregation of MWCNTs has been studied, however the effect of perfluorinated surfactants at low concentration is uncertain. To understand this interfacial phenomenon, the influences of perfluorooctanoic acid (PFOA), and sodium dodecyl sulfate (SDS) as a control, on MWCNT aggregation in the aqueous phase were examined by the UV absorbency method. Influences of pH and cationic species on the critical coagulation concentration (CCC) value were evaluated. The CCC values were dependent on the concentration of PFOA, however a pronounced effect of SDS concentration on the CCC values was not observed. The CCC values of the MWCNTs were 51.6 mmol/L in NaCl and 0.28 mmol/L in CaCl2 solutions, which suggested pronounced differences in the effects of Na+ and Ca2+ ions on the aggregation of the MWCNTs. The presence of both PFOA and SDS significantly decreased the CCC values of the MWCNTs in NaCl solution. The aggregation of the MWCNTs took place under acidic conditions and was not notably altered under neutral and alkaline conditions due to the electrostatic repulsion of deprotonated functional groups on the surface of the MWCNTs.