In contrast to the disordered body-centered cubic (bcc) A2 phase, the ordered face-centered cubic (fcc) L12 phase exhibits negative magnetostriction (λ) and has a high elastic modulus (E). Therefore, an in-depth understanding of the microstructural evolution of Fe–Ga thin films from bcc A2 phase to fcc L12 phase is essential to obtain Fe–Ga thin films with desirable properties. The transformation of the phase structure, magnetic domain structure, and magnetic properties of Fe72Ga28 thin films is analyzed in this study. The phase transformation of the Fe72Ga28 thin film from A2 to A2 L12 occurred after heat treatment, as determined by high-resolution transmission electron microscopy (HRTEM) and glancing-incidence X-ray diffraction (GI-XRD). Non-continuous lattice distortion at the phase boundaries of A2 and L12 was also observed, as shown by geometric phase analysis (GPA) and electron backscattered scattering detection (EBSD). Numerous edge dislocations at the phase boundaries were revealed by HRTEM. A shift in the magnetic domain structure from the maze-like domain to maze-like domain and honeycomb-like domain was detected by magnetic force microscopy (MFM). The variation in magnetic properties was determined to be related to the structural transformation and ununiform lattice distortion between the phase boundaries of the A2 and L12.