In unmanned aircraft applications, electromagnetic wave (EMW) absorbers suffer from defects in narrow absorption bands and poor mechanical properties. To solve the problems, a lightweight multilayer stealth structure with wide broadband absorption performance and excellent mechanical properties was designed and prepared by adjusting microscopically the number of multi-walled carbon nanotubes (MWCNT) and modulating macroscopically the thickness-matching relationship of the structure to promote the absorption of EMW synergistically. Under the MWCNT of 30 wt% and the depletion layer with the thickness of 0.2 mm, the effective absorption bandwidth (EAB) covers the entire Ku-band while maintaining a minimum reflection loss (RL) of −15 dB. Besides, the radar cross-sectional area attenuation is as high as 23.1 dBm2, as well as the mechanical properties of the radar absorbing structures (RAS) were improved significantly due to the reducing structural density from balsa wood and the enhancement effect of glass fiber mats (GFM). The study constructed balsa-based RAS with excellent EMW absorbing and mechanical properties from both micro-nano scale and macro-structure, providing a research route for designing high-performance and lightweight stealth structures.