An atomic-scale understanding of the role of strain on the microstructural properties of nanoscale precipitates will be helpful to explore the precipitation behavior as well as the structure-property relationships in crystalline multi-phase systems. Nanoscale Si precipitates are formed in Al-based alloys prepared by selective laser melting. The phase structure and the nature of heterointerface have been characterized using advanced electron microscopy. The nanocrystalline Si mainly contains two polymorphs, diamond-cubic Si (DC-Si) and 4H hexagonal Si (4H-Si). Heteroepitaxy occurs at the DC-Si(111)/Al(100) and 4H-Si(0001)/Al(100) interfaces in terms of a coincidence-site lattice model. The nanocrystalline Si undertakes tensile strain superposed by the matrix through heterointerfaces, facilitating the formation of 4H-Si in the nanoscale crystallite, which provides a strategy for designing Si polymorphic materials by strain engineering.