As the application of the MEMS parts increases, the structural safety of MEMS appears importantly. A lot of MEMS parts are made by a multi-grain silicon wafer, which is an orthotropic material. Moreover directions of the materials on each grain are distributed randomly. The stress analysis for the multi-grain is important factor in order to apply the MEMS parts to industrial applications. The finite element method (FEM) is commonly used by a stress analysis method but the boundary element method (BEM) is known as the result of the BEM is more accurate than that of the FEM since the fundamental solution are used. In this study, we derived the boundary integration equation for the orthotropic material by applying fundamental solutions with complex variables. The multi-region analysis procedure for the BEM and the multi-grain generation procedure by a random process technique are developed in order to apply the analysis of the multi-grain orthotropic material. The discontinuous element is used in order to remove the comer problem in the BEM. The results of the present method are compared with those of the finite element method in order to verify the present procedure.