An accurate estimation of residual stresses is crucial to ensure dimensional accuracy and prevent premature fatigue failure of 3D printed components. Different from their crystalline counterparts, the effect of residual stress would be worse for amorphous alloys owing to their intrinsic brittleness with low fracture toughness. However, the generation of residual stress and its performance in 3D printed amorphous alloy components still remain unclear. Here, a finite element method combined with experiments and theoretical analyses was introduced to estimate the residual stress in selective laser melting of a Zr-based amorphous alloy. The results revealed that XY cross scanning strategy exhibits relatively low residual stress by comparison with X and Y strategies, and the residual stress becomes serious with increasing bar thickness. The residual stress, on the other hand, could be tuning by annealing or preheating the substrate. The above scenario is thoroughly understood according to the temperature gradient mechanism and its effect on microstructure evaluation.