Gold nanoparticles (AuNPs) with excellent surface-enhanced Raman spectroscopy (SERS) activities were prepared using sulfur, selenium and nitrogen (S, Se, and N)-doped carbon dots (S-, Se-, and N-CDs) as both reducing and capping agents. S-, Se-, and N-CDs rich in surface functional groups were synthesized using D-penicillamine (D-PA), citric acid, sodium selenate (NaSeO), and ethylenediamine as precursors by a facile microwave digestion method. The specific interaction of S-, Se-, and N-CD-based AuNPs (AuNPs/Se-CDs) and 6-methylnicotine (6-MN), which is attributed to the formation of S-Au and Se-Au bonds, contributes to the development of a highly sensitive and specific surface-enhanced Raman scattering (SERS) sensing platform for detecting 6-MN, with a low detection limit of 0.13 μg L. This platform was effectively applied for the determination of 6-MN in electronic cigarette samples.