This paper aims to reveal the relationship among low-temperature toughness, microstructure and secondary crack from both microstructural and crystallographic perspectives. Instrumented Charpy tests were carried out in the upper platform, transition temperature range, as well as at lower temperatures. Quantitative fractographic analysis, microstructural characterization and secondary crack observation were conducted on half of the impact specimen. Crystallographic features were identified in the secondary crack proximity, e.g. variant selection, orientation relationship, cleavage plane of the corresponding crack matrix. Some results in literature are confirmed. Nickel addition is beneficial to hindering crack propagation as a result of microstructure improvement. The most effective barrier for crack propagation is high-angle misorientation boundaries between Bain packets and the boundaries of ferrite matrix with the microstructure of granular bainite. Additionally, high-angle misorientation boundaries between closed-packed plane packets arrest cracks in the mixed microstructure of fine lath bainite and intricate acicular ferrite. Most preferred crack propagation planes are {110} and {100} in our low carbon bainitic weld metals, with the decreasing possibility of {112} and {123}.