Conventional radar-absorbing structure is typically manufactured with high weight percentage (wt.%) of carbonaceous nano-conductive particles in the polymer matrix to tailor its microwave absorbing performance. However, these manufacturing methods have some physical limitations with regard to fabrication, due to the high viscosity in the polymer matrix and, inhomogeneous in mechanical and electrical properties. No study has been conducted with micro-mechanical failure prediction of radar-absorbing structure dispersed with multi-walled carbon nanotubes. In order to address these limitations, radar-absorbing structures dispersed with multi-walled carbon nanotubes were designed in the Ku-band (12.4–18 GHz). Additionally, to establish and verify the micro-mechanical failure analysis based on multiscale modeling, finite element analysis was carried out using the Mori–Tanaks mean-field homogenization model within the representative volume element model in the microstructure. In order to verify the Hashin criteria of radar-absorbing structure dispersed with multi-walled carbon nanotube (0.5 wt.%, 1.0 wt.% and 1.5 wt.%), mechanical tests (tensile, compressive and shear test) were conducted according to ASTM standards. In this paper, radar-absorbing structure with irregularly arranged filler and matrix with representative volume element was modeled from the micro-mechanical point of view and the results from Hashin failure criterion were verified both by simulations and experimental results of prediction strengths within the expected error range (lower than 6%). The reliability of application in micro-mechanical prediction of radar-absorbing structure was confirmed considering the multi-scale modeling.