A two-dimensional super-cell phononic crystal semi-active isolator based on magnetorheological elastomers is designed, which can be used for vibration isolation of mechanical devices at medium and high frequencies. The plane wave expansion method of the super-cell is introduced to model the dynamic characteristics of the proposed phononic crystal isolator. The influence of the constituent materials, dimension parameter of the super-cell, and magnetic field intensity on the band structure is investigated by the plane wave expansion method. The results show that the change of material will affect the bandgap frequency of the super-cell and the dimension parameter of the super-cell will affect the bandgap formation mechanism. It is worth pointing out that the bandgap frequency and width of the isolator can be adjusted by controlling the applied current of the magnetorheological elastomer. Therefore, this method offers a broad range of possibilities for phononic crystal vibration isolation design.