Methyltrimethoxysilane (MTMS) based silica aerogels (MSA) with a controllable skeleton size were synthesized in pure water via adjusting the cetyltrimethylammonium bromide (CTAB) content. The results show that the content of CTAB has little effect on the surface chemical composition of MSA, while the skeleton size and pore size of MSA decrease with increasing the CTAB content. The average skeleton diameter (d) of MSA decreases from 2.39 μm to 0.55 μm, and the adsorption capacity for organic liquids decreases simultaneously when the CTAB content increases from 0.01 g to 0.03 g. When the CTAB content is 0.01 g, the as-prepared MSA has good adsorption properties for alcohols and alkanes, where the maximum adsorption capacity reaches 10 g/g, the adsorption rate of the pumping application is 1.04 g/s, and the capillary rise speed of organic liquids can reach 2.1 mm/s. Furthermore, the high thermal stability (456 ℃) of MSA ensures the realization of thermal desorption. A preparation method of MSA with a controllable skeleton size to obtain aerogels with specific adsorption properties.