This paper focuses on the residual stress in a lithium niobate (LN) film layer of a LN-on-insulator (LNOI)/Si hybrid wafer. This stress originates from a large mismatch between the thermal expansion coefficients of the layers. A modified surface-activated bonding method achieved fabrication of a thin-film LNOI/Si hybrid wafer. This low-temperature bonding method at 100 °C showed a strong bond between the LN and SiO2 layers, which is sufficient to withstand the wafer thinning to a LN thickness of approximately 5 μm using conventional mechanical polishing. Using micro-Raman spectroscopy, the residual stress in the bonded LN film in this trilayered (LN/SiO2/Si) structure was investigated. The measured residual tensile stress in the LN film layer was approximately 155 MPa, which was similar to the value calculated by stress analysis. This study will be useful for the development of various hetero-integrated LN micro-devices, including silicon-based, LNOI-integrated photonic devices.