An efficient methodology is introduced for rapid analysis and design of three-dimensional (3-D) doubly periodic structures over a wide frequency range based on hybrid finite element boundary integral (FEBI) methods. The 3-D doubly periodic structures can be represented as nonorthogonal lattices composed of general inhomogeneous bianisotropic media with arbitrarily-shaped metallic patches. Based on Floquet theory and periodic boundary conditions, the original stated problem that involves infinite periodic structures can be converted into a single unit cell. Using the equivalence principle, the derived BI equation formulation is applied to the top and bottom surfaces of the unit cell, which results in a perfectly reflectionless boundary condition for the FE-based approach. Then, the unit cell was meshed using triangular prismatic volume elements, which provide a great deal of flexibility in modeling complex planar geometries with arbitrary shapes in the transverse direction. The adaptive integral method (AIM) was employed to accelerate the calculation of the matrix-vector product for the BI portion within the iterative solver. Furthermore, a model-based parameter estimation (MBPE) technique was proposed for the wide-band interpolation of the required impedance matrix elements in the BI part for near field components that were used in the AIM procedure. The accuracy and efficiency of the proposed hybrid algorithms are demonstrated by the presented numerical results (e.g., in comparison with analytical solutions). Several simulation results are presented to illustrate the flexibility of the proposed methods for analysis of frequency selective surfaces with arbitrarily-shaped metallic patches, bianisotropic materials, and nonorthogonal lattice configurations.Index Terms-Adaptive integral method (AIM), bianisotropic media, finite element, frequency selective surface (FSS), hybrid finite-element boundary integral (FEBI) methods, integral equation, model-based parameter estimation (MBPE), periodic structure, periodic structure with nonorthogonal lattice.