The impact toughness of low-Cr heat-resistant steel weld metal is an important problem to broaden the application of low-Cr heat-resistant steel. In this study, the microstructure and impact toughness of 12Cr1MoVR low-alloy heat-resistant steel weld metals with various boron contents (B1 = 0.0028%, B2 = 0.0054%, and B3 = 0.0079%) were investigated. The microstructures of all weld metals were composed of block ferrite, carbides, and inclusions. Results indicated that with increased B content, prior austenite grain sizes decreased, and minor microstructure changes could be found. With the increase in B content from 0.0028% to 0.0054% to 0.0079%, the ductile–brittle transition temperature of the weld metals decreased from 30 to 0 to −14 °C, the toughness of weld metal increased, and the hardness slightly decreased, all of which are directly related to the refinement of prior austenite grain size because of the addition of B content. However, on the top-shelf zone, such as at the testing temperature of 80 °C, ductile fracture dominates the fracture surface; with the increase in B content, the size and density of inclusions increased gradually, which led to the decrease of the impact toughness at 80 °C when the B content was 0.0079%.