This paper presents the characterization of bearing failure mechanisms in composite joints with countersunk bolt by applying an X-ray Computed Tomography (XCT) technique and a developed bearing failure model to build the physical mechanisms into the framework of continuum damage mechanics (CDM) in our composite bolted and bonded analysis tool for Abaqus (CB2ATA). The high-fidelity XCT was explored for the detection and characterization of bearing failure in bolted composite components without removing the fastener, which could introduce significant scatter in XCT scan due to its high density, compared with lightweight carbon fiber reinforced polymer (CFRP) composite laminates. A static bearing model was also developed for the damaged material response in the bearing region based on a micromechanics analysis in the longitudinal and transverse directions. In this study, single shear bearing (SSB) tests was firstly executed with XCT scan, and then progressive failure analyses were performed to explore the effects of bolt failure on the interaction of the intra- and inter-ply damages. The predicted load-displacement response was compared with experimental measurement, and the simulated failure patterns were compared with the XCT images. A new design was proposed using the enhanced analysis tool to achieve a dominant bearing failure mechanism on the basis of the current SSB test.