The development of high-performance flame-retardant materials with better thermal insulation properties is of great significance to modern building energy conservation. In this study, we report the facile and scalable fabrication of novel aerogels (SA-HGM-APP) based on the building blocks of ammonium polyphosphate (APP) coated hollow glass microspheres (HGM) and matrix material sodium alginate (SA) by freeze drying method. The as-prepared composite aerogel exhibits better thermal stability (decomposition temperature over 210°C). In addition, SA-HGM-APP composite aerogels have good thermal insulation properties and low thermal conductivity, which is 0.035 W m−1 K−1. More importantly, the peak heat release rate (pHRR) is 14.14 kW m−2, the limiting oxygen index (LOI) value is as high as 100%, and the aerogel composite material can reach UL-94 V-0 grade, so it shows excellent flame retardancy. These results attributed to a synergistic effect, which combines the rich porous structure derived from HGM, so that SA and APP have better thermal insulation and excellent non flammability, thus providing excellent flame retardancy. SA-HGM-APP aerogel composite has many advantages, such as simple preparation method and high mechanical strength. It has great potential in future thermal insulation and flame retardancy applications.