Four metal powder flux-cored wires with added nickel (Ni) were designed to systematically investigate how Ni influences the microstructure and toughness in low-carbon bainitic weld metals (WMs). The microstructure was safely predicted by utilizing reasonable welding craft parameters (i.e., appropriate heat input and proper interpass temperature). Microstructural characterization, crystallographic analysis, microhardness mapping, fracture microparameter measurement, and finite element method calculations were all taken into account. This work showed that more martensite transformation occurs with increasing Ni and that the ductile-brittle transition temperature drops with added Ni. The boundaries with low-angle misorientation (i.e., less than 4°) enhance microhardness and the optimal inclusion size is in the range of 0.3–0.45 μm, thus revealing the reasons for the resulting microhardness and toughness variations. In addition, the high-angle grain boundaries in close-packed plane packets effectually prevent cracks. From a practical perspective, 4 wt.% Ni could be the best design for welding wires in the present work. This work confirmed many of the results found in recently published literature. These results provide a reference for the composition design of welding wires and the processing method of WMs.