In this paper, we present an efficient and accurate approach to predict the shielding effectiveness (SE) of an enclosure with numerous small apertures, which involves two methods: the equivalent model of aperture array and waveguide equivalent circuit model. First, the equivalent model of aperture array is derived from the numerical simulation that simplifies the aperture array into a single aperture, then the equivalent single aperture's impedance is calculated and the equivalent circuit model is applied to calculate the SE of the enclosure. The result shows a better agreement with the measurement than the original waveguide equivalent circuit model. In comparison with aperture's admittance model, our method can be applied to the square, circular, and rectangular apertures with nonuniform small aperture distribution. The proposed method can also significantly reduce the simulation time and improve the efficiency of simulation compared with the generalized modal method of moments and CST. Finally, we discuss the applicability of this method.