Based on the tight-binding model and the Greens function method, the effects of atomic disorder of lattice configuration and the orientation disorder of side radical spins on the spin polarized transport through a metal/organic-ferromagnet/metal structure are investigated. The results show that the atomic disorder reduces the threshold voltage of the device and suppresses the conducting current. The staircase structure of the current-voltage curve for a molecular device is eliminated when the disorder is enhanced. The current keeps a high spin polarization if the atomic disorder is not strong. The orientation disorder of side radical spins reduces the spin splitting of molecular energy levels, which increases the threshold voltage of the device. The current and its spin polarization are reduced apparently at a low bias when the strength of disorder is enhanced. We further simulate the effect of temperature on the spin polarized transport through the device by taking into account two kinds of disorders.