The Fe-rich heterogeneous microstructures were observed in the weld metal (WM) of laser welding on dissimilar metals between 9Cr steel and alloy 617, manifesting as vortex-like and lamellar-like structures. They displayed a face-centered cubic structure and consisted of cellular and columnar dendrites. The vortex-like structure was distributed on the upper side of the WM and exhibited the solidification grain boundary. Due to the higher liquid temperature and insufficient mixing, the vortex-like structure exhibited preferential nucleation during the solidification process. On the other hand, the lamellar-like structure was situated on the lower side of the WM and had a thickness of 50 μm. The lamellar-like structure and WM solidified simultaneously with the rapid solidification rate, resulting in noticeable intergranular chemical segregation. During the tensile test, deformation twins formed in the heterogeneous microstructure, due to the lower stacking fault energy and fine particles. Numerous deformation twins played a crucial role in inhibiting crack initiation, which performed the same orientation. Furthermore, the heterogeneous microstructure generated 89.8% of twin boundaries during the crack propagation, while the WM had 30.4%. This phenomenon facilitated plastic energy absorption and deflected the crack propagation path. Thus, the heterogeneous microstructures contributed to the enhancement of mechanical toughness at room temperature.