The invention is applicable to the technical field of sonar, and provides a seabed sonar reference beacon positioning method and device and a seabed positioning system, and the method comprises the steps: determining the coordinates of a transducer according to the attitude data of a measurement ship, the information of a lever arm and the coordinates of a GNSS antenna, and carrying out the epoch matching processing; according to the sound velocity profile data and the acoustic time measurement data, determining a back-and-forth sound velocity sound path distance between a transducer sound signal transmitting moment and a transducer sound signal receiving moment and the seabed reference beacon; according to the coordinates of the transducer, the approximate coordinates of the seabed sonar reference beacon and the sound velocity profile data, carrying out sound ray bending correction processing on the back-and-forth sound velocity sound path distance; and constructing a two-way sound path model to position the seabed sonar reference beacon according to the coordinates of the transducer, the approximate coordinates of the seabed sonar reference beacon and the back-and-forth sound velocity sound path distance. According to the method, the data quality is controlled by preprocessing the multi-source data, the change of the position of the transducer in the acoustic signal propagation process is considered, acoustic ray bending correction is carried out through acoustic ray tracking, the error influence is weakened, and the positioning precision is improved.