We report a new strategy for the gram-scale synthesis of highly blue fluorescent nitrogen and sulfur embedded organic dots through one-pot hydrothermal condensation of citric acid (CA) with cysteamine (Cys) at 200 °C. Under such circumstance, the dehydration between CA and Cys produces a molecular fluorophore, which self-assembles to amorphous dots through hydrophobic interaction and π–π stacking. In aqueous solution, the dots exhibit a very high fluorescent quantum yield that is above those of most photoluminescent carbon dots to date, since the fluorophore is not carbonized. The intense fluorescence emission is achieved by establishing an efficient push–pull fluorophore system, as revealed by first-principles simulations. In the solid phase, the fluorescence of the dots is severely attenuated. More importantly, unlike excitation-independent emission displayed in solution, the fluorescence of the organic dots in the aggregated solid state is dependent on excitation wavelength, which is quite a rare and unique phenomenon. Finally, this new kind of organic dots has shown diverse applications in sensing and imaging.