Due to the complexity of traditional Chinese medicines (TCMs), it is very important to develop a method that can recognize anthraquinones, the active ingredients in TCMs, with high selectivity. Here, a molecularly imprinted fluorescence sensor was coated on the surface of carbon quantum dots (CDs). Allobarbital was used as functional monomer for this application using theoretical calculations and was successfully synthesized and characterized. The template molecule chrysophanol was combined with the functional monomer allobarbital using a hydrogen bond array. Then, a series of adsorption experiments were performed to study the specific recognition of anthraquinones by the prepared sensors. The results showed that the prepared sensor had a good linear response to concentrations of chrysophanol in the concentration range 0.5 mg · L-1 to 8.0 mg · L-1, a low detection limit (5.0 μg · L-1), high stability, and a short response time (20 min). Additionally, the obtained fluorescence sensor was successfully applied to selectively recognize anthraquinones in TCMs with recoveries of 90.1% to 101.7%. The prepared sensor displays excellent sensitivity and high selectivity towards anthraquinones, mainly due to the specific hydrogen binding sites for the target molecules. Overall, this fluorescence sensor can selectively recognize anthraquinones in TCMs, and provide a method for quality monitoring and rational utilization of TCMs.