An effective medium modeling technique is proposed to homogenize the periodic objects embedded in layered media. The homogenization is based on the same scattering coefficients. An integral equation based approach is adopted to solve the scattering problem of original structures. Our modeling results are compared with Maxwell-Garnett mixing formula and published results. Good agreements have been observed. Periodic metal patches embedding in layered dielectric structure is fabricated and measured to validate the modeling technique. The difference between experiment results and proposed modeling results is less than 3%.