An equivalent damage model was established to study the fatigue damage behavior of steel–aluminum friction stir welding (FSW) joints. Internal defects of friction stir welding joint under various cyclic loading stages were observed by X-ray microcomputed tomography (X-CT). For the characteristics of defects of the steel–aluminum FSW joints, a simplified method of defects considering key parameters is proposed, and then, the defect model is established. The FSW joint model was established based on the steel–aluminum boundary contour identified by using image processing techniques. Based on the defect model and the FSW joint model, the equivalent damage model was developed. The equivalent damage model was subjected to finite element analysis and compared with the test using strain amplitude as the damage variable. The equivalent damage model can be used to assess fatigue damage in steel–aluminum FSW joints, which provides some theoretical basis for fatigue life prediction.