Fluorescent nitrogen-doped carbon dots (CDs) were prepared via hydrothermal method at 190 °C for 10 h using rhizobium from soy as the carbon and nitrogen source. Their optical properties, structure, morphology, and functional groups were characterized in detail and the results showed that they possess unique excitation-dependent fluorescence behavior, with average diameter 4.5 ± 2.0 nm and good water dispersibility. Due to the overlap of the UV-vis absorbance of chlortetracycline hydrochloride (CCH) and the fluorescence excitation band of CDs, the fluorescence of the prepared CDs can be quenched by CCH selectively and sensitively. The changes of the fluorescence intensity of CDs have a good linear relationship with the concentration of CCH in a wide concentration range of 5-100 μM, with a detection limit of 0.254 μM. This present method has been successfully applied to determine the CCH in water with recovery ranging from 96.0% to 100.7%.