Carbon quantum dots (CQDs) have attracted enormous interest in recent years owing to their low cytotoxicity, excellent biocompatibility and strong fluorescence. They have been successfully employed in sensor, bio-imaging, and drug carrier applications. A complete understanding of their core-surface structure is essential for tuning their physical and chemical properties for various applications. Conventional characterizations of CQDs are conducted with electron microscopy or spectroscopy, such as transmission electron microscopy, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy and Raman spectroscopy. However, these techniques cannot fully resolve the core-surface structure of CQDs. In this study, we attempt to analyze the structures of CQDs by laser desorption/ionization mass spectrometry (LDI-MS) using three model CQDs synthesized from citric acid (CA-CQDs), diammonium citrate (AC-CQDs) and spermidine trihydrochloride (Spd-CQDs). Both CA-CQDs and AC-CQDs produced anionic carbon cluster ions ([Cn]-, n = 4-9) during the laser desorption/ionization process. Additionally, AC-CQDs produced fragments containing C, N, and O that appeared at m/z values of 41.999, 91.015, and 107.008, which were identified by 15N isotopes as [CNO]-, [CH3N2O3]-, and [CH3N2O4]-, respectively. By contrast, subjecting Spd-CQDs to the same analysis did not yield carbon cluster ions ([Cn]-); instead, strong chlorine-associated ions with a unique isotopic pattern were observed, strongly implying that Spd-CQDs contain chlorine. The lack of carbon cluster ion formation in nitrogen- and chlorine-doped Spd-CQDs indicates that nitrogen and chlorine are abundantly and homogenously doped in the CQDs. We also found a shot-dependent fragmentation behavior for AC-CQDs that produces nitrogen- and oxygen-containing ions and carbon cluster ions ([Cn]-) during initial fragmentation of the surface, with a gradual destruction of the nanocrystalline carbon core after additional shots. These results suggest that LDI-MS can be used as a tool for analyzing the core-surface structure of CQDs, particularly when it contains a heteroatom doped carbon core with various surface functional groups containing nitrogen, oxygen and halogens.