The cross-section effect leads to variations in the microstructure and thickness of marine engineering steel thick plates, which may result in delaminated tearing and a reduction in material plasticity and fracture toughness. The microstructural characterization of the matrix and the regions near the impact fracture at different depths by the thickness of the thick plate, as well as the crack propagation mechanism, was investigated. The low-temperature fracture toughness at the surface, quarter-thickness, and center at -40 °C were found to be 204 J, 215 J, and 98 J, respectively. Near the impact fracture, the grains of the test steel exhibit significant deformation. The grains at the surface experience fragmentation, leading to grain refinement and the formation of serrated cracks. At the quarter-thickness, cracks display large-angle deflection, and the deflection at the center is notably reduced, accompanied by an increase in the number of voids. In this study, the influence of the cross-section effect on the fracture toughness of marine engineering steel thick plates is thoroughly investigated. The experimental results provide theoretical guidance for the design and production of thick plates with optimal strength and toughness. This study primarily examines the influence of the cross-section effect on the microstructure and low-temperature fracture toughness of the investigated steel. Furthermore, it not only examines the microstructure of the base metal but also employs electron backscatter diffraction (EBSD) technology to characterize and analyze the microstructure near the crack, thereby exploring the influence of the cross-section effect on the fracture mechanism of the investigated steel.