Amino/hydroxyl-functionalized fluorescent carbon nanodots (C-NanoD) are conveniently synthesized based on hydrothermal carbonization of chitosan at 180°C. Dialysis membranes with small cut-off masses (500-1000 Da) were found useful for removing the side-products and low molecular mass species to purify the C-NanoD product. Herein, reversed-phase high-performance liquid chromatography (RP-HPLC) has been successfully applied to fractionate the C-NanoD product. The elution order of the C-NanoD species present in the sample follows approximately their core sizes from small to large. The separated C-NanoD fractions are collected and characterized by UV absorption spectroscopy, photoluminescence (PL) spectroscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and transmission electron microscopy (TEM). All the C-NanoD fractions display a distinctive absorption band at 300 nm, attributing to the n→π* transition of C=O bond. The PL spectra of the fractions display emission peaks at 400-415 nm which are slightly red-shifted with their increase in relative molecular masses. The C-NanoD fractions are fully anatomized by MALDI-TOF MS, displaying their fragmentation mass ion features. The core sizes of some selected C-NanoD are determined as 1.6, 1.8, 2.5, and 3.1 nm by TEM which are in consistent with their HPLC elution order. The findings highlight the virtues of RP-HPLC to fractionate and reveal the unique characteristics of individual C-NanoD species present in an as-synthesized C-NanoD product which may have potential applications in the fields of bioanalysis, bioimaging, catalysis, chemosensing, energy storage, and optoelectronics device.