The BeiDou Navigation Satellite System (BDS) features a heterogeneous constellation so that it is difficult to mitigate the multipath in the coordinate-domain. Therefore, mitigating the multipath in the observation-domain becomes more important. Sidereal filtering is commonly used for multipath mitigation, which needs to calculate the orbit repeat time of each satellite. However, that poses a computational challenge and damages the integrity at the end of the multipath model. Therefore, this paper proposes a single-difference model based on the multipath hemispherical map (SD-MHM) to mitigate the BDS-2/BDS-3 multipath in a short baseline. The proposed method is converted from double-difference residuals to single-difference residuals, which is not restricted by the pivot satellite transformation. Moreover, it takes the elevation and the azimuth angles of the satellite as the independent variables of the multipath model. The SD-MHM overcomes the unequal observation time of some satellites and does not require specific hardware. The experimental results show that the SD-MHM reduces the root mean square of the positioning errors by 56.4%, 63.9%, and 67.4% in the east, north, and vertical directions; moreover, it contributes to an increase in the baseline accuracy from 1.97 to 0.84 mm. The proposed SD-MHM has significant advantages in multipath mitigation compared with the advanced sidereal filtering method. Besides, the SD-MHM also features an excellent multipath correction capability for observation data with a period of more than seven days. Therefore, the SD-MHM provides a universal strategy for BDS multipath mitigation.