Selective laser melting (SLM) has potential to prepare complex shaped amorphous alloy parts, however, the almost inevitable crystallization makes it very difficult to obtain excellent performance parts. Most of previous studies focus on improving properties by optimizing parameters such as laser power, scanning speed, and scanning strategy. As is well known, the substrate is an important component in SLM devices, which directly supports and contacts the initial powder and melting pool, affecting the absorption and transfer of heat, the formation and cooling of the melting pool, and therefore exerts a significant influence on the quality and microstructure of printed parts. However, there is relatively little research on its influence. It is important and necessary to understand the influence of substrate temperature on crystallization behavior of Fe-based amorphous alloy during SLM process. Molecular dynamics (MD) simulations can provide direct evidence for the evolution of clusters and band pairs, which can help clarify the crystallization mechanism and alleviate the crystallization. In this work, the influence of substrate temperature on the crystallization and evolution of atomic clusters in Fe₅₀Cu₂₅Ni₂₅ amorphous alloy during SLM is investigated on an atomic scale, using MD simulation under different substrate temperatures (300–900 K), laser power values (500–800 eV/ps), and scanning speeds (0.1–1.0 nm/ps). The research results show that when the substrate temperature is lower than 750 K, the content of characteristic bond pair 1421 and the corresponding $ \left\langle{0,{\mathrm{ }}4,{\mathrm{ }}4,{\mathrm{ }}6}\right\rangle $ cluster increase with the substrate temperature rising, thereby increasing face-centered cubic bond pair and cluster and promoting the crystallization. When the substrate temperature rises to a value close to the glass transition temperature, the evolution of bond pairs and clusters becomes complex, which is influenced by the collaborative and competitive effects, such as the ability to form glass, melting and cooling rate. This work reveals the evolution of atomic clusters and band pairs in the SLM process of Fe-based amorphous alloys, and the initiation of crystal phases at different substrate temperatures, providing new ideas for understanding and regulating crystallization.