In this Letter, a novel mechanism to enhance the magnetoelectric (ME) coupling between electric polarization and magnetism using the dynamic Jahn-Teller (JT) effect is demonstrated. Electric polarization of over 100 μC/m2 is induced by the magnetic field owing to the second-order ME effect in the noncentrosymmetric transition metal complex [MnIII(taa)]. This appearance of electric polarization does not require magnetic order in contrast to the linear ME effect in ME multiferroic materials. The value of the electric polarization is 1 order larger than that induced by the second-order ME effect, which originates from the p-d hybridization. Our calculation, taking into account the single-ion-type magnetic anisotropy originating from the spin-orbit interaction and ferrodistortive intermolecular interaction, verifies that the alignment of the JT distortion by the magnetic field results in the large electric polarization observed. Thus, our results provide a new method to gain strong ME coupling by tuning the atomic displacement using a magnetic field.