The honeycomb (HC) core of sandwich structures undergoes flexural loading and carries the normal compression and shear. The mechanical properties and deformation response of the core need to be established for the design requirements. In this respect, this article describes the development of the smallest possible representative cell (RC) models for quantifying the deformation and failure process of the Nomex polymer-based hexagonal HC core structure under the out-of-plane quasi-static loadings. While the hexagonal single and multi-cell models are suitable for the tension and compression, a six-cell model is the simplest RC model developed for shear in the transverse and ribbon direction. Hashin’s matrix and fiber damage equations are employed in simulating the failure process of the orthotropic cell walls, using the finite element (FE) analysis. The FE-calculated load–displacement curves are validated with the comparable measured responses throughout the loading to failure. The location of the fracture plane of the critical cell wall in the out-of-plane tension case is well predicted. The wrinkling of the cell walls, leading to the structural buckling of the HC core specimen in the compression test, compares well with the observed failure mechanisms. In addition, the observed localized buckling of the cell wall by the induced compressive stress during the out-of-plane shear in both the transverse and ribbon direction is explained. The mesoscale RC models of the polymer hexagonal HC core structure have adequately demonstrated the ability to predict the mechanics of deformation and the mechanisms of failure.