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The impact of conventional and microwave annealing (CA and MA, respectively) on MgTiO3 thin films sputtered on a silicon substrate has been investigated by Raman spectroscopy. This article studies the impact of temperature, time, and atmosphere used for CA and MA on the structural properties of these layers. The results show that the MgTiO3 film crystallinity is better after an MA performed at 800 °C for 5 min under air atmosphere. At the same time, the oxygen vacancies density in the layer is lower. Moreover, the occurrence of the TiO2, Mg2TiO4, and MgTi2O5 phases after CA and MA is strongly dependent on the temperature, time, and atmosphere of the annealing process as well as the type of annealing. To our knowledge, this is the first time that the impact of MA on the structural properties of MgTiO3 films has been compared to that of CA and studied by Raman spectroscopy.