The asymmetric epoxidation of indene catalyzed by Jacobsen catalysts with different axial ligands (Cl − , Br − , OAc − , CF 3 CO 2 − , N(CH 3 ) 2 − , and NO 3 − ) was theoretically investigated. The spin states and approach vectors were taken into consideration. The axial ligands can affect the steric conformation of the catalysts. Furthermore, the structure distortion during the formation of the transition state is responsible for the enantioselectivity, and this distortion is also highly related to the axial ligands. These ligands have nonnegligible influence on both the catalytic activity and enantioselectivity. Changing the axial ligand can even turn the enantioselectivity from (S, R)-to (R, S)-enantiomer. The influence of axial ligand on the enantioselectivity is comparable with that induced by the salicylidene ring modification. Controlling the catalytic activity and enantioselectivity of salen-Mn complexes by simply changing the axial ligand deserves to be paid more attention.