We propose in this paper a novel hybrid numerical modeling method for computing electromagnetic scattering from inhomogeneous targets containing honeycomb structures. In the proposed approach, the whole honeycomb structure is divided into the inner and outer two subregions. Each thin wall of a unit cell in the outer subregion is replaced by a zero-thickness surface, with the aid of a resistive sheet boundary condition (RSBC) to describe the electric and magnetic field discontinuities across the surface. Each unit cell in the inner subregion is homogenized by using the Hashin–Shtrikman and the Mori–Tanaka formulae. The two subregions are further divided into smaller subdomains by introducing the Robin-type transmission condition to couple subregion interfaces, as well as subdomain interfaces. The whole solution region is then discretized and solved using the nonconformal domain decomposition-based hybrid finite element–boundary integral–multilevel fast multipole algorithm (FE-BI-MLFMA). The numerical results demonstrate that the proposed approach exhibits a high accuracy, efficiency, and flexibility. Solutions of scattering by a wing-like object and a practical unmanned aerial vehicle (UAV) model with honeycomb radar-absorbing structures are presented, showing the superior performance of the proposed algorithm.