Carbon nanodots (Cdots) have aroused widespread concerns in the field of biomedical applications. In order to achieve better implications of behavior of Cdots in the biological environment, an array of spectroscopic, electrochemical and calorimetric techniques were performed to study the interaction of Cdots possessing different charges with human serum albumin (HSA) in physiological condition. Two polymer, polyethylene glycol (PEG) and polyetherimide (PEI), were applied to passivate the bare Cdots to achieve the Cdots with different surface charge, namely negatively charged PEG Cdots and positively charged PEI Cdots. The fluorescence of HSA was obviously quenched by both Cdots in a charge-independent behavior through a dynamic collision mechanism. Moreover, the association affinity of PEG Cdots or PEI Cdots bound to HSA was very close to each other. In addition, PEG Cdots with diverse content exhibited little effects on the secondary structure of HSA while only high content of PEI Cdots induced obvious conformation perturbation of HSA. The electrostatic forces dominate the association between HSA and PEI Cdots while the association of PEG Cdots to HSA is initiated by hydrophobic and van der Waals forces. Furthermore, the results of isothermal titration calorimetry revealed that both the interaction was driven by favorable entropy and enthalpy, which confirmed that these association processes are thermodynamically spontaneous. Finally, the sites marker competitive experiment showed that the association sites of Cdots with HSA exhibit a charge dependent manner, namely PEG Cdots effectively occupy the site I of HSA while the association sites of PEI Cdots are mainly located in site II.