Fluorescent carbon nanodots (CDs) have been highlighted as promising semiconducting materials due to their outstanding chemical and optical properties. However, the intrinsic heterogeneity of CDs has impeded a clear understanding of the mechanisms behind their photophysical properties. In this study, as-prepared CDs are fractionated via chromatography to reduce their structural and chemical heterogeneity and analyzed through ensemble and single-particle spectroscopies. Many single particles reveal fluorescence intensity fluctuations between two or more discrete levels with bi-exponential decays. While the intrinsic τ components are uniform among single particles, the τ components from molecule-like emissions spans a wider range of lifetimes, reflecting the inhomogeneity of the surface states. Furthermore, it is concluded that the relative population and chemical states of surface functional groups in CDs have a significant impact on emissive states, brightness, blinking, stability, and lifetime distribution of photoluminescence.