The thermal safety of hydrophobic silica aerogels (SAs) is essential to thermal insulation applications. Herein, trimethylchlorosilane (TMCS), dimethyldichlorosilane (DMDCS), and methyltrichlorosilane (MTCS) were employed as surface modifiers to prepare three different methylsilyl-modified SAs (i.e., TSA, DSA, and MSA) and their combustion characteristics and thermal hazards were experimentally studied in detail. The cone calorimeter test found that the three SAs have similar combustion processes and the variations in ignition time and fire spread rate with the heat flux obey simple logarithmic and linear relationships, respectively. It further found that TSA has the most methylsilyl groups on silica skeletons and thus has the largest heat release, followed by DSA and MSA in turn, implying that TSA has the greatest fire hazard among the three SAs. These results further demonstrate that the type and quantity of methylsilyl groups on the skeletons of SAs significantly affect the thermal hazard of methylsilyl-modified SAs. In addition, the combustion mechanism of the methylsilyl-modified SAs is discussed. In total, this work experimentally studies the combustion characteristics of methylsilyl-modified SAs and compares their thermal hazards, clarifying the potential fire risk of methylsilyl-modified SAs in practical thermal insulation applications.