Three dimensional reconstruction and finite element method are combined to study the damage behavior of aluminum alloy resistance spot welded joints. Fatigue damage of spot welded joints under different cyclic loading stages was obtained by X-ray microcomputed tomography (X-ray micro CT). Then, Avizo software was used to reconstruct the scanned data of joints with different damage degrees, and the distribution and variation of defects in the joints are obtained. On this basis, three-dimensional finite element damage models were established. Finite element calculations were carried out to analyze the fatigue damage of spot welded joints by adopting the effective elastic modulus as the damage parameter. The results show that the effective elastic modulus is consistent with the experimental results. The method of combining 3D reconstruction with finite element method can be used to evaluate the internal damage of spot welded joints and provide theoretical basis for the prediction of fatigue life.