Ceramic aerogels have attracted significant attention in the field of high-temperature insulation. However, most ceramic aerogels suffer from inadequate mechanical properties and limited stability at temperatures below 1000 °C, which limit their application. In this study, an assembly strategy was designed. Mullite whisker aerogels (MWAs) with excellent resistance to high temperature and thermal stability were prepared by utilizing mullite nanowhiskers as assembly units and a small amount of silica sols as high-temperature binders. The MWAs exhibit remarkably low thermal conductivity (0.039 W/(m·K) at room temperature and 0.067 W/(m·K) at 600 °C) and minimal shrinkage at elevated temperatures (only 3.33% shrinkage rate after calcination at 1600 °C for 30 min). The MWAs exhibit excellent thermal stability, withstanding temperatures as high as 1600 °C. In addition, we developed core–shell whisker assembly units composed of mullite@silica to fabricate aerogels, resulting in materials with enhanced mechanical strength (compressive strength of 0.81 MPa), remarkable chemical stability even under continuous exposure to high temperatures, and improved temperature resistance due to the core–shell structure. These characteristics make them highly suitable for utilization as superinsulating materials in extremely high-temperature environments.