Capillary zone electrophoresis (CZE) coupled with UV absorption and laser-induced fluorescence detections has been applied to study the complexity of carbon nanodots (C-dots) products synthesized with microwave-assisted pyrolysis of citric acid (CA) and 1,2-ethylenediamine (EDA). The effects of pH and concentration of run buffer on the CZE separation of C-dots are studied in detail. The optimal acetate run buffer (30mM, pH 3.6) is subsequently employed to investigate the effect of reaction time and mole ratio of amine (NH 2 ) to carboxylic acid (COOH) moieties of the precursors on the C-dots species present in C-dots products. Our results confirm that the synthesis of C-dots could be improved by lengthening the microwave irradiation time and optimizing the initial mole ratio of NH 2 /COOH in the precursors. Negatively charged C-dots are obtained only when the amount of CA exceeds that of EDA, i.e., the mole ratio of NH 2 /COOH is 0.25–0.80. By contrast, when the quantity (mole) of NH 2 in EDA is equal to or larger than that of COOH in CA, only positively charged and neutral C-dots species are formed, inferring that the C-dots species are predominantly covered by the surface-attached ammonium and amido moieties. This work highlights the merit of CZE to identify the composition of an as-prepared C-dots product which is pretty much dependent on the mole ratio of NH 2 /COOH. It is anticipated that our CZE methodology will open a new avenue in optimizing the synthetic conditions for producing specific C-dots of desired composition.