The interface between an Mn-doped gamma-gallium oxide (Ga2O3) thin film and an MgAl2O4 (001) substrate has been investigated using high-resolution transmission electron microscopy (HRTEM), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), and first-principles calculations. A high-quality Mn-doped gamma-Ga2O3 film with a defective spinel structure has been epitaxially grown by pulsed laser deposition. The gamma-Ga2O3 crystal shows an uniform tetragonal distortion with a tetragonality of 1.05 throughout the film thickness of 75 nm. HRTEM and HAADF-STEM observations reveal that the gamma-Ga2O3 and MgAl2O4 crystals form a coherent interface without any interfacial layers or precipitates. The atomistic structure and energies are theoretically evaluated for the interfaces with two types of termination plane, i.e., Mg- and Al2O4-termination of MgAl2O4. The cation sublattice is found to be continuous for both interfaces despite the defective spinel structure of Mn-doped gamma-Ga2O3 with some vacant cation sites. The Al2O4-termination shows a lower interfacial energy than the Mg-termination under most conditions of the chemical potentials. This behavior is attributed to the energetic preference of the Mn-Al2O4 local configuration at the interface.