SiC aerogels have great potential as thermal insulation materials and wave absorbers owing to high porosity and excellent dielectric properties. Recently, many SiC based electromagnetic wave absorbers with excellent performance have been developed. However, the coordination of thermal insulation, mechanics and electromagnetic wave absorption remains a challenge. Reasonable skeleton design and interface engineering are effective methods to overcoming this challenge. Herein, we report a mechanically strong SiC aerogel with hollow SiC microtube skeletons and SiC-SiO2 heterogeneous structures through engineering its microstructure by a simple continuous sintering-etching-annealing process. Accordingly, the aerogel exhibits excellent mechanical properties with a maximum compressive stress of 2.86 MPa. In addition, the aerogel shows an ultra-low thermal conductivity of 0.028 W/(m·K). More importantly, the aerogel exhibits a wide-band absorption band of 6.7 GHz at a matching thickness of 3.3 mm. Therefore, the findings of this study not only provide a simple method for the microstructure regulation of SiC aerogels but also provide a new technique to enhance electromagnetic wave absorption by using heterogeneous interface engineering.