The welding performance of shipbuilding steel under large heat input could be improved greatly by the addition of Mg to the steel, but the impact toughness of the heat affect zone (HAZ) is not stable. According to the three different thickness steel plates obtained in the industrial experiment, the large heat input welding was carried out by different heat input, and the impact toughness analysis, impact fracture analysis, metallographic microstructure analysis and inclusions analysis were carried out. The results showed that, the HAZ of three kinds of thickness plates induced much intragranular acicular ferrite (IAF); with Mg addition, the inclusion dimension had been reduced effectively, and the IAF-induced ability of the inclusions had also been improved. The difference of HAZ impact toughness with different welding heat input and different impact temperature is significant; considering the influence of welding heat input and metallographic microstructure on the impact toughness of HAZ, the welding heat load had a far greater effect than the metallographic microstructure on ductile–brittle transition temperature. At the same time, if the original metallographic microstructure of steel was coarse, the pinning effect of the inclusions would be reduced significantly, and the microstructure of HAZ would be coarsened and the impact toughness of HAZ would be decreased, so there is a certain matching relationship between the metallographic microstructure and the inclusion dimension.