The B,N dual-doped carbon dots (B,N-CDs) for ratiometric fluorescence detection the morin were prepared from sodium tetraborate and polyethyleneimine through the single-step hydrothermal method. The B,N-CDs exhibited the optimum excitation and emission wavelength at 340 nm and 467 nm, respectively. Interestingly, the intensities of emission peak at 467 nm of B,N-CDs reduced meanwhile a new peak emerged at 560 nm with the continuous addition of morin, which revealed the ratio fluorescence characteristic between F_560nm/F_467nm and morin concentration with the linearity range and detection limit of 14.5–32.5 μmol/L and 0.3 μmol/L (S/N = 3), respectively. The interference of common antibiotics and remedies could be ignored when the concentration of morin was detected by the B,N-CDs, which demonstrating the outstanding selectivity. Furthermore, the proposed fluorescence method is used to detect morin in urine with recoveries are 99.8–104.5%. The results of this research indicate the feasibility and practicality of B,N-CDs as an effective fluorescent probe for the determination of morin.