In this study, using synchrotron radiation X-ray imaging, the microstructure, tensile properties, and fatigue properties of FGH96 nickel-based superalloy were tested, and the fatigue damage mechanism was analyzed. An analysis of the experimental results shows that the alloy structure is dense without voids or other defects. It was observed that the primary γ′ phase is distributed on the grain boundary in a chain shape, and the secondary γ′ phase is found inside the crystal grains. The X-ray diffraction (XRD) pattern indicates that no other phases were seen except for the γ and γ′ phases. The tensile strength of the alloy is 1570 MPa and the elongation is 12.1%. Using data fitting and calculation, it was found that the fatigue strength of the alloy under the condition of 5 × 106 cycles is 620.33 MPa. A fatigue fracture has the characteristics of secondary crack, cleavage step, fatigue stripe, tire indentation, and dimple. The fracture is a mix of cleavage fracture and ductile fracture. Through a three-dimensional reconstruction of the alloy synchrotron radiation imaging area, it was found that the internal defects are small and mostly distributed at the edge of the sample. The dimple morphology is formed by cavity aggregation and cavity germination resulting from defects in the material itself, fracture of the second-phase particles, and separation of the second-phase particles from the matrix interface. By analyzing the damage mechanism of fatigue fractures, it is concluded that the cleavage step is formed by the intersection of cleavage planes formed by branch cracks, with the main crack of the confluence extending forward to form a cleavage fracture. The crack propagation path was also analyzed, and under the action of cyclic load and tip passivation, the crack shows Z-shaped propagation.