The main purpose of this chapter is to propose a new boundary element formulation for the modeling and optimization of three-temperature nonlinear generalized magneto-thermoelastic functionally graded anisotropic (FGA) composite microstructures' problems, which is the gap of this study. Numerical results show that anisotropy and the functionally graded material have great influences on the nonlinear displacement sensitivities and nonlinear thermal stress sensitivities of composite microstructure optimization problem. Since, there are no available data for comparison, except for the problems with one-temperature heat conduction model, we considered the special case of our general study based on replacing threetemperature radiative heat conductions with one-temperature heat conduction. In the considered special case, numerical results demonstrate the validity and accuracy of the proposed technique. In order to solve the optimization problem, the method of moving asymptotes (MMA) based on the bi-evolutionary structural optimization method (BESO) has been implemented. A new class of composite microstructures problems with holes or inclusions was studied. The two-phase magnetothermoelastic composite microstructure which is studied in this chapter consists of two different FGA materials. Through this chapter, we investigated that the optimal material distribution of the composite microstructures depends strongly on the heat conduction model, functionally graded parameter, and shapes of holes or inclusions.