We improve thermal tolerance of a Co/Pt based synthetic ferrimagnetic (SyF) reference layer in a CoFeB/MgO-based perpendicular anisotropy magnetic tunnel junction by employing a surface modification treatment (SMT) using Ar plasma on a Pt buffer layer underneath the SyF layer. A higher perpendicular anisotropy and more robustness against annealing for the SyF reference layer is observed by the employment of SMT. From the cross-sectional scanning transmission electron microscope of the magnetic tunnel junction and atomic force microscopy on the Pt buffer layer, SMT has no significant effect on the surface roughness of the Pt buffer layer. On the other hand, X-ray diffraction analysis reveals that SMT increases the lattice spacing of the Pt buffer layer and shrinks that of the Co/Pt multilayer, which are maintained after annealing at 400 °C. Those structural changes could lead to the improvement of perpendicular anisotropy and thermal tolerance against annealing. A high-resolution Rutherford backscattering analysis reveals that Ar ions used for SMT penetrate to the Pt buffer layer, resulting in variation of the lattice spacing for the Pt buffer layer and Co/Pt multilayer. In addition, suppression of Fe diffusion from the CoFeB reference layer to the bottom Co/Pt multilayer is observed by using energy dispersive X-ray spectrometry, which also contributes to the higher thermal tolerance against annealing. The present observation reveals that the employment of SMT enables one to obtain both high perpendicular magnetic anisotropy and high robustness against annealing through crystallographic change of the Co/Pt multilayer and suppression of Fe diffusion from CoFeB layer into the Co/Pt multilayer.