Owing to their extraordinary photophysical properties, carbon dots (CDs) have found applications across various fields, including bioimaging, sensing, and environmental research. Despite huge application potential, the fabrication of CDs still lacks the desired control at the molecular level, and precise structural regulation towards property-tailored CDs remains elusive. The mechanistic details of nucleation, growth, and carbonization processes leading to CDs are still unknown, with key thermodynamic and kinetic parameters yet to be revealed. Herein, we performed quantum chemical calculations of explicitly micro-hydrated reaction systems to thoroughly explore the mechanism of a prototypical reaction of citric acid and ethylenediamine. The theoretical results showed activation barriers and thermodynamics along the reaction pathway, thus helping identify key heterocyclic intermediates and cyclization products. The cyclization and condensation reactions were further simulated