A simple heat treatment method was used to optimize the three-dimensional network structure of the hydrophobic aerogel, and during the heat treatment process at 200–1000 °C, the thermal conductivity of the aerogel reached the lowest to 0.02240 W/m·K between 250 °C and 300 °C, which was mainly due to the optimization of microstructure and pyrolysis of surface groups. Further Fluent heat-transfer simulation also confirmed the above results. Synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) was used to finely measure the pyrolysis process of aerogels, and the pyrolysis process of aerogel was divided into four stages. (I) Until 419 °C, as the temperature continued to rise, surface methyl groups were oxidized to form hydroxyl. (II) As the temperature reached to 232 °C, the oxidation proceeded. In addition, inside the aerogel, because of lacking oxygen, the reaction produced CH4 and C–Si bonds would form. (III) After 283 °C, Si–OH groups began to condense to form Si–O–Si, which optimized the three-dimensional network structures to be beneficial to improve the thermal insulation performance of silica aerogel. (IV) When it reached 547 °C, the chemical reaction was terminated, and all the primary particles gradually fused into secondary particles and sintered to form clusters.