The scratching mechanism of polycrystalline γ-TiAl alloy was investigated at the atomic scale using the molecular dynamics method, with a focus on the influence of different grain sizes. The analysis encompassed tribological characteristics, scratch morphology, subsurface defect distribution, temperature variations, and stress states during the scratching process. The findings indicate that the scratch force, number of recovered atoms, and pile-up height exhibit abrupt changes when the critical size is 9.41 nm due to the influence of the inverse Hall-Petch effect. Variations in the number of grain boundaries and randomness of grain orientation result in different accumulation patterns on the scratch surface. Notably, single crystal materials and those with 3.73 nm in grain size display more regular surface morphology. Furthermore, smaller grain size leads to an increase in average coefficient of friction, removed atoms number, and wear rate. While it also causes a larger range of temperature values and distributions. Due to the barrier effect of grain boundaries, smaller grains exhibit reduced microscopic defects. Additionally, average von Mises stress and hydrostatic compressive stress at the indenter tip decrease as grain size decreases owing to grain boundary obstruction. This work is helpful to better understand the deformation mechanism of polycrystalline γ-TiAl alloy during the nano-scratching process.