We investigate the spin current through a molecular quantum dot (MQD) irradiated with a rotating magnetic field and an oscillating magnetic field by nonequilibrium Green's function. The rotating magnetic field rotates with the angular frequency $\omega_r$ around the $z$-axis with the tilt angle $\theta$, and the time-oscillating magnetic field is located in the z-axis with the angular frequency $\omega$. Different behaviors have been shown in the presence of electron-phonon interaction (EPI) which plays a significant role in the transport. The spin current displays asymmetric behavior as the source-drain bias $eV=0,$ novel side peaks or shoulders can be found due to the phonon absorption and emission procedure, and the negative spin current becomes stronger as the parameter $g$ increases. However, the spin currents display the same magnitude and the same oscillation behavior in the region $\mu_0B_1>3\Delta$ regardless of the parameter $g.$