Baicalin, a flavonoid compound extracted from the rhizome of Scutellar iae Baicalensis, plays a vital role in improving liver function after injury, reducing liver disease and treating primary liver cancer, which is also the first SARS-CoV-2 3CLpro virus inhibitor according to the latest research data published in BioRxiv. Therefore, constructing a simple and highly sensitive analytical method for the determination of baicalin is of great significance for the clinical and pharmacy settings. Herein, for the first time, carbon dots are explored for baicalin detection. Using biomass waste grape peels as the organic carbon source, nitrogen-doped fluorescent carbon dots (PT-NCDs) were fabricated, which were synthesized perfectly by a simple, environmentally friendly and one-step solid-phase thermal method without adding any other organic or acid/base reagents. Based on the synergistic effect of photo-induced electron transfer and dynamic quenching, a quenched fluorescence sensor for the determination of baicalin with a good linear range of 0.1–20 μM and a satisfactory detection limit of 43.8 nM was constructed, which successfully quantified trace amount of baicalin in baicalin capsules, human serum and urine samples. The results indicate that PT-CDs are expected to become potential sensing materials for the real-time monitoring of baicalin in organisms, which is very important for our health.