3D fatigue crack opening and propagation behaviors in an Al-Mg-Si alloy have been inyestigated in this study. A combined methodology of an in-situ 3D crack visualization via the synchrotron X-ray CT and image-based numerical simulation which takes into account real crack morphology has been applied for the study. The complex crack morphology has been observed and many essential features of the crack and its opening/propagation inside the material have been identified. Typical example would be the complex deformation behaviors in the region where two crack segments lying on different horizontal planes overlap each other. The image-based numerical simulation was performed to investigate the interactions of two overlapping crack segments and their influences on the region next to overlapping region. The combined methodology of the in-situ 3D crack visualization and the image-based numerical simulation has been demonstrated to be powerful and feasible in revealing and understanding various fracture phenomena inside materials.