Honeycomb structures of shape memory alloy (SMA) have become one of the most promising materials for flexible skins of morphing aircraft due to their excellent mechanical properties. However, due to the nonlinear material and geometric large deformation, the SMA honeycomb exhibits significant and complex nonlinearity in the skin and there is a lack of relevant previous research. In this paper, the nonlinear properties of the SMA honeycomb structure with arbitrary geometry are investigated for the first time for large deformation flexible skin applications by theoretical and experimental analysis. Firstly, a novel theoretical model of SMA honeycomb structure considering both material and geometric nonlinearity is proposed, and the corresponding calculation method of nonlinear governing equations is given based upon the shooting method and Runge–Kutta method. Then, the tensile behaviors of four kinds of SMA honeycomb structures, i.e., U-type, V-type, cosine-type, and trapezoid-type, are analyzed and predicted by the proposed theoretical model and compared with the finite element analysis (FEA) results. Moreover, the tensile experiments were carried out by stretching U-type and V-type honeycomb structures to a global strain of 60% and 40%, respectively, to perform large deformation analysis and verify the theoretical model. Finally, experimental verification and finite element validation show that the curves of the theoretical model results, experimental results, and simulation results are in good agreement, illustrating the generalizability and accuracy of the proposed theoretical model. The theoretical model and experimental investigations in this paper are considered to provide an effective foundation for analyzing and predicting the mechanical behavior of SMA honeycomb flexible skins with large extensional deformations.