Using ab initio nonadiabatic molecular dynamics simulation, we have studied the time-dependent charge transport dynamics in a single-molecule junction formed by gold (Au) electrodes and a single benzene-1,4-dithiol (BDT) molecule. Two different types of charge transport channels are found in the simulation. One is the routine non-resonant charge transfer path, which occurs in several picoseconds. The other is activated when the electronic state of the electrodes and that of the molecule get close in energy, which we refer to as the resonant charge transport. More strikingly, the resonant charge transfer occurs in an ultrafast manner within 100 femtoseconds, which notably increases the conductance of the device. Further analysis shows that the resonant charge transport is directly assisted by the B2 and A1 molecular vibration modes. Our study provides atomic insights into the time-dependent charge transport dynamics in single-molecule junctions, which is important for designing highly efficient single-molecule devices.