In this work, X90 pipeline steel was welded by shielded metal arc welding with root and submerged arc welding with calk and cap. After that, the joint was tempered at 550 °C and 600 °C. Subsequently, the microstructure and mechanical properties were investigated by optical microscope, scanning electron microscope (SEM) and Vickers hardness tester. The fracture surface of welded joint was analyzed by SEM. The experiments show that: After high-temperature tempering treatment, the Widmanstatten structure disappears in coarse-grained region. The number of lath martensite in the original structure of the welded joint decreases, and the quantity of granular bainite increases. The acicular ferrite disappears gradually and the polygonal ferrite grains increase, and the M/A island components decompose into fine grains with the increase in tempering temperature. The mechanical properties of the joints also change and the hardness rises because of the disappearance of Widmanstatten structure improves after heat treatment, and yield strength and tensile strength of the specimens have the lowest values after tempering at 550 °C. After tempering at 600 °C, the hardness decreases and strength–ductility reaches 11,571 MPa%. The tensile fracture of 600 °C sample presents delamination and ductile fracture. Through comparative analysis, it can be concluded that the plasticity and toughness of multilayer welded joints after tempering at 600 °C is improved, and they have better comprehensive mechanical properties.