This study aims to investigate the synergistic effect of Ni-Mo contents on microstructural evolution in super-high strength steel weld metals, and its following influence on toughness is also explored through crystallographic analysis. The results indicate that the microstructures of both weld metals are acicular ferrite, grain boundary ferrite, ferrite side-plate and bainitic ferrite. Compared with high-Ni–Mo weld metal, the decrease in Ni–Mo content increases the acicular ferrite fraction instead of bainitic ferrite. The crystallographic characteristics confirm that the adjacent parallel bainitic ferrite tend to be in the single Bain group in variant selection, while adjacent interlocking acicular ferrite belonged to multiple Bain groups. The multiple Bain groups contribute high-density large-angle grain boundaries, leading toughness improvement in low-Ni–Mo weld metal.