Carbon dots (CDs) possess abundant functional groups on their surface which are related to their application in various fields such as sensing, imaging, and catalysis. Understanding the amount and properties of these functional groups and their interaction with metal ions is essential but has posed longstanding challenges because of the diverse and complex structures of CDs. In this work, potentiometric titration is demonstrated as an effective method to figure out the categories and amounts of functional groups. Surface complexation modeling with the FITEQL program was applied to the quantification of the surface sites on CDs with the titration data. Then with the obtained molar concentrations of the surface sites, the pKas of these surface sites were calculated with the Hyperquad program. Finally, titration experiments of CDs with and without Fe(III) were carried out and the stability constants of Fe(III) and ArgCDs were simulated on the Hyperquad program. By utilizing the stability constants, the distribution of Fe(III) species at different pHs and the concentrations of Fe(III) and CDs were also investigated. This potential method might be used for characterizing the surface sites on other CDs or even other soluble nanoparticles as well as for investigating the interactions of the surface sites with different metal ions.