Although bolted jointsbetween aluminum alloy (Al) and carbon fiber reinforced plastic (CFRP) are often used in engineering, the specific cause of fatigue failure in these joints is still not understood. The tension–tension fatigue experiments were performed on CFRP/AL bolted single lap joints (SLJs) at high load levels in this investigation. Two stacking sequences ([±45]12 and [0/90, ±45]3s), were developed together with multiple load levels LR ranging from 0.75 to 0.96. Micro X-ray computed tomography (µCT) was used for non-destructive testing, three-dimensional (3D) models were reconstructed, and pores were measured and assessed to further explore the fatigue failure mechanism of CFRP. The results showed that although CFRP failed at greater load levels, Al failures occurred at lower load levels. At a ratio of 0.923 to 0.95, a competitive failure was also observed. The results of CT analysis showed that holes appeared to start and grow significantly in the ± 45 layer. Pores will enlarge and agglomerate when the load level and number of cycles increase. This research investigated how CT technology can be used in CFRP fatigue experiments.