In this study, the nano-deformation behavior of semi-solid Al-Si alloy was investigated using a molecular dynamics simulation as a part of the research on the surface crack behavior in thixoformed automobile parts. The microstructure of the grain-size controlled Al-Si alloy consists of primary and eutectic regions. In eutectic regions the crack initiation begins with initial fracture of the eutectic silicon particles and inside other intermetallic phases. Nano-deformation characteristics in the eutectic and primary phase of the grain-size controlled Al-Si alloy were investigated through the molecular dynamics simulation. The primary phase was assumed to be single crystal aluminum. It was shown that the vacancy occurred at the zone where silicon molecules were.