Dimensional tolerance is an important factor for the geometry quality of products. The stiffness matrices of sheet metal components are usually not variational during the process of tolerance analysis; however, material properties of the compliant parts may change in volume production. The variation of the part thickness changes the part stiffness matrix so that the sensitivity matrix is different from that of the assembly with nominal thickness. The paper proposes an improved sensitivity matrix between the incoming part variation and the assembly variation for the assembly with thickness variation. Moreover, the orthogonal design is used to judge the importance of part and thickness variation for the assembly deviation. The proposed method is illustrated through a case study and the results show that the thickness variation influences the relationship between the part variation and the assembly variation. In addition, part variation plays a more important role to assembly variation than the thickness deviation does according to the orthogonal design.