| Due to the influence of quantum size effect and surface effect, silicon nanowires (SiNWs) have unique mechanical, electrical and coupling properties, and thus become core components of nanoelectronic devices. However, surface defects are inevitable in the preparation of SiNWs. In this paper, the effects of the surface defect concentration on Young's moduli of SiNWs with different cross-section shapes (squares, hexagons and triangles) along the  and  crystal orientations were investigated by molecular dynamics method. The results show that when the SiNW has only one surface defect on the surface, Young's moduli of SiNW in different crystal orientations decrease linearly with the increase of the defect concentration. When the surface defect concentration is 10%, the decrease of Young's modulus is between 10% and 20%, which is closely related to the crystal orientation and cross-section shape of SiNW. When there are multiple surface defects, Young's moduli show the different ﬂuctuation trends with the increase of defect concentration. Young's modulus of the triangular SiNW fluctuates the most, and the variation of the square SiNW is small, that is to say, the difference of the defect distribution has little effect on Young's modulus of the square SiNW, which indicates that the effect of surface defects is closely related to their distributions and cross-section shape. By comparing with experimental results, our results reveal that surface defects are an important factor that leads to the small Young's modulus experimental value of SiNW. Therefore, when characterizing the mechanical properties of SiNW, the effects of surface defects need to be considered.