Abstract: The mechanism of intermetallic compounds (IMCs) along the thickness direction on crack formation in thick plate Al/Mg friction stir welded (FSW) joints remains unresolved. This study investigates the effects of strain gradient, mismatch, and fracture toughness on crack formation. The results indicate that the cracks are exclusively formed in the upper of the stir zone and at the Al/Al₃Mg₂ interface. Crack formation in the upper of the stir zone is associated with the eutectic reaction (Al + Al₃Mg₂ ↔ Liquid). The Al/Al₃Mg₂ interface exhibits the highest lattice mismatch (δ = 2.27%) and misorientation gradient (0.7°), which corresponds to the preferential crack initiation site. In addition, nanoindentation tests confirm that the Al₁₂Mg₁₇ phase (0.41 MPa·m^1/2) possesses higher fracture toughness than the Al₃Mg₂ phase (0.28 MPa·m^1/2). Therefore, controlling the thickness of the Al₃Mg₂ phase is essential for suppressing crack formation. These findings provide a theoretical basis for crack suppression in thick Al/Mg FSW joints and are value for further improving joint quality.