In this study, [Co/Ni]2/PtMn thin films with different PtMn thicknesses (2.7 to 32.4 nm) were prepared on Si/SiO2 substrates. The post-deposition perpendicular magnetic field annealing (MFA) processes were carried out to modify the structures and magnetic properties. The MFA process also induced strong interlayer diffusion, rendering a less sharp interface between Co and Ni and PtMn layers. The transmission electron microscopy (TEM) lattice image analysis has shown that the films consisted of face-centered tetragonal (fct) PtMn (ordered by MFA), body-centered cubic (bcc) NiMn (due to intermixing), in addition to face-centered cubic (fcc) Co, Ni, and PtMn phases. The peak shift (2-theta from 39.9° to 40.3°) in X-ray diffraction spectra also confirmed the structural transition from fcc PtMn to fct PtMn after MFA, in agreement with those obtained by lattice images in TEM. The interdiffusion induced by MFA was also evidenced by the depth profile of X-ray photoelectron spectroscopy (XPS). Further, the magnetic properties measured by vibrating sample magnetometry (VSM) have shown an increased coercivity in MFA-treated samples. This is attributed to the presence of ordered fct PtMn, and NiMn phases exchange coupled to the ferromagnetic [Co/Ni]2 layers. The vertical shift (Mshift = −0.03 memu) of the hysteresis loops is ascribed to the pinned spins resulting from perpendicular MFA processes.