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Silicon–germanium (SiGe) alloy is a new semiconductor material of great interest in thermoelectric devices, optoelectronic devices, infrared detectors, and semiconductor industry. In the present work, molecular dynamics simulation was conducted to investigate the deformation behavior in nano-scratching of SiGe alloy. The effect of scratching direction and Ge composition on material removal mechanism was discussed, aiming to understand the nanoscale deformation mechanism of SiGe alloy. The simulation results indicate that the machining direction and Ge composition have significant influences on the atomic flow and chip formation during nano-scratching. Besides, less subsurface damage and elastic recovery are observed when scratching along the (011)[100] direction with higher Ge composition. The highest crystal purity of the machined surface is achieved when scratching on the Si60Ge40 workpiece. Furthermore, the Ge composition has a significant influence on the workpiece temperature due to the variation of the thermal conductivity of the workpiece. This work could enrich the understanding of the deformation mechanism of SiGe alloy during nanoscale machining and open a potential to improve the machining performance of multicomponent semiconductor materials.