Polar transport ships frequently traverse in the brash ice channel opened by icebreakers. Although the substantial ice resistance caused by direct collisions with the level ice is avoided, the hull still encounters collisions with the brash ice, leading to periodic damage and exacerbating the fatigue issues of the hull structure. To address the fatigue challenges faced by ships sailing in the brash ice channels, this paper proposes an ice-induced fatigue damage assessment method based on the CFD-DEM-FEM. Referring to the brash ice model test conducted at the Hamburg Ship Model Basin (HSVA), a discrete element ice model and a numerical brash ice tank are established using the CFD-DEM coupling method. The simulated ship-ice interaction is compared with HSVA’s experimental results to validate the reliability of the numerical brash ice tank and ice load. The ice load time history resulting from the ship-brash ice collision is applied to the hull, and the hot spot stress time history under each fatigue sub-condition is calculated using the FEM. The improved rain-flow counting method is employed to determine the stress level of the hot spot stress time history, and the S-N curve method based on the linear cumulative damage criterion is used to calculate the total fatigue damage of hot spots. Finally, the results of the proposed method are compared with those of the LR method. This study can serve as a valuable reference for the ice-induced fatigue assessment of ships navigating in brash ice channels.