Nickel oxide (NiO) has been historically misinterpreted as containing rhombohedral-like features, leading to structural ambiguity. Here, NiO epilayers of varying thickness were grown on sapphire to investigate the strain-driven domain evolution. At the initial stage (∼22 nm), compressive strain from oxygen sublattice mismatch stabilizes a uniform pseudo-rhombohedral appearance, atomically identified as high-density cubic antiphase domains. With increasing thickness, strain relaxes and neighboring antiphase domains merge via stacking inversion induced by dislocation glide, producing aligned cubic NiO with serrated boundary fronts under local strain inhomogeneity. Beyond 120 nm, the upper layer becomes fully aligned cubic phase with vanishing pseudo-rhombohedral features, accompanied by increased dislocation density up to 3.17 × 1010 cm−2. These results clarify the microscopic origin of pseudo-rhombohedral domains in FFC NiO and guide epitaxy for developing low-defect oxide heteroepitaxial devices.