In this paper, an equivalence principle algorithm combined with the characteristic basis function (CBF) method has been developed to efficiently analyze the finite periodic arrays composed of uniaxial dielectric materials and conducting objects. Three kinds of the CBFs for each equivalent surface and its surrounding object are simultaneously constructed using multiple plane wave illuminations and singular value decomposition technique, and thus memories related to the scattering and translation operators are significantly saved, while retaining good computational accuracy. Numerical results of a frequency selective conducting array, a uniaxial dielectric cube array, and a periodic array of the composite object including a uniaxial rod and a split ring resonator are given to illustrate good performance of proposed method.