In this study, water-soluble ammonium polyphosphate- (APP) and methyl trimethoxysilane (MTMS)-modified industrial bamboo residue (IBR)-derived holocellulose nanofibrils (HCNF/APP/MTMS) were used as the raw materials to prepare aerogels in a freeze-drying process. Synthetically modified aerogels were confirmed by Fourier transform infrared spectroscopy, X-ray diffraction, and thermal stability measurements. As-prepared HCNF/APP/MTMS aerogels showed themselves to be soft and flexible. The scanning electron microscopy (SEM) analysis showed that the foam-like structure translates into a 3D network structure from HCNF aerogels to HCNF/APP/MTMS aerogels. The compressive modules of the HCNF/APP/MTMS aerogels were decreased from 38 kPa to 8.9 kPa with a density in the range of 12.04–28.54 kg/m3, which was due to the structural change caused by the addition of APP and MTMS. Compared with HCNF aerogels, HCNF/APP/MTMS aerogels showed a high hydrophobicity, in which the water contact angle was 130°, and great flame retardant properties. The peak of heat release rate (pHRR) and total smoke production (TSP) decreased from 466.6 to 219.1 kW/m2 and 0.18 to 0.04 m2, respectively, meanwhile, the fire growth rate (FIGRA) decreased to 8.76 kW/s·m2. The thermal conductivity of the HCNF/APP/MTMS aerogels was 0.039 W/m·K. All results indicated the prepared aerogels should be expected to show great potential for thermally insulative materials.