The magnetohydrodynamic (MHD) simulation is often applied to study the global dynamics and configuration of a planetary magnetosphere for the space weather. In this paper, the computational performance of MHD code is evaluated with 128 nodes Xeon Phi KNL of Cray XC40. As the results, the 2D and 3D domain decompositions of SoA (structure of array) make the effective performances and AoS (array of structure) and hybrid parallel computation become low performances. Adding the performance optimizations for Xeon Phi to our MHD simulation code, then we have obtained 2.4 % increase of execution efficiency in total and we achieved 3 TFlops performance gain using 128 nodes.