High-energy beam welding was introduced for pipeline steel welding to reduce pipeline construction costs and improve the efficiency and safety of oil and gas transportation. Microstructures and their distribution in X100 laser-welded joints, which determine the joints’ strength and toughness, are discussed in this paper. Welded joints were prepared by an automatic 10,000-watt robot-based disc laser-welding platform for 12.8 mm thick X100 pipeline steel. Then, the grain, grain boundary, orientation, and distribution pattern of each zone of the welded joints were studied by optical microscopy (OM), scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), and electron backscattered diffraction (EBSD) analysis techniques. The results showed that the grain boundary density, contents of the high-angle and low-angle grain boundaries, distribution states, and evolution trends of coincident site lattice (CSL) grain boundaries were essentially the same in each zone from the base metal (BM) to the weld of the X100 pipeline steel laser-welded joint. The relative content of grain boundaries above 55°, which were composed of the Σ3 type CSL grain boundary, showed a considerable impact on the mechanical properties of the joint. The content of twin grain boundaries was closely related to the thermal cycles of laser welding, and the effect of the cooling rate was greater than that of the process of austenization.