In this research, the fatigue damage behavior under three-point bending of a composite joint incorporating a single countersunk fastener is investigated. Firstly, a self-developed fatigue test system was set up to test the fatigue characteristics of CFRP-countersunk bolted assembly under the displacement amplitude cycles of 103 to 106 to study the formation and expansion rule of damage and cracks. It found two typical damage processes, both of which involve some formal interface damage between fiber and matrix. Based on the experiment, a finite element fatigue damage analysis on this assembly was carried out according to the Hashin failure criterion. The simulation result shows an identical fatigue damage location and fatigue life with the experimental phenomenon. Moreover, it predicted the final fatigue life of the specimen under 10 hz cyclic loading with 1 mm displacement and 10 Nm bolt preloading. This research provides guidance for the engineering fatigue issues of single-bolted joint composite connection structures and provides a reference for the corresponding technical specifications formulation.