An optimal layered inhomogeneous background which can be used in an embedded microwave tomography system is proposed. The method is based on a new evaluation method of integral radiation operator with respect to an configuration and optimal methods such as simulated annealing method. First, the integral radiation operator is calculated using the finite element method. Then, a kind of metric which can be used to evaluate the operator is proposed. The metric contains information about the whole singular value spectrum of a integral radiation operator. A set of synthetic researches is performed to show the correlation between the metric and inversion error. The method can evaluate an integral radiation operator using a number, and it can be used in optimal process easily as the cost function. Simulated annealing method is employed to obtain the permittivity of each layer in the optimal layered inhomogeneous background. Finally, synthetic researches are employed both on simple target and complex target to test the optimal layered inhomogeneous background. The results show that the optimal layered inhomogeneous background can expedite the convergence process and more accurate inversion results can be obtained.