Research on the development of flexible silica aerogels (FSAs) has been ongoing due to their excellent thermal insulation, low density, and high elasticity. However, the physical properties of FSAs, such as density, thermal conductivity, mechanical strength, and surface wettability, are highly dependent on the preparation conditions. To achieve the desired properties of FSAs for various applications, it is necessary to develop a method to fine-tune their physical properties. In this paper, two modifiers of methyltrimethoxysilane (MTMS)/trimethylethoxysilane (TMES) were employed to fine-tune the bulk density of a series of flexible silica aerogels (FSAs), reflecting a series of FSAs with fine-tunable physical properties. First, the precursor was synthesized by a click reaction between vinyltrimethoxysilane (VTMS) and 2,2′ (ethylenedioxy) diethanethiol (EDDET). The VTMS, EDDET, and the as-prepared precursor were characterized by FT-IR and NMR spectroscopy. Subsequently, the precursor was converted into a series of FSAs (denoted by FSA, FSA-M, and FSA-T) through conventional sol-gel reactions with/without MTMS/TMES. Chemical structures of synthesized FSAs were confirmed by13C and29Si solid-state NMR spectroscopy. The porous structure of FSAs was identified by BET and SEM, respectively. Physical properties, such as thermal conductivity, mechanical strength, and surface wettability of FSAs were determined by a Hot Disk, durometer/DMA in compression mode, and contact angle measurements, respectively. This study found FSAs containing none, 1 wt%, 5 wt%, and 10 wt% of MTMS increase the density of FSAs from 0.419 g/cm3(FSA), 0.423 g/cm3(FSA-M1), 0.448 g/cm3(FSA-M5), and 0.456 g/cm3(FSA-M10). It should be noted that the thermal conductivity, surface hardness, bulk mechanical strength, and hydrophobicity of FSA-Ms of increasing MTMS loading were all found to show a rising trend, while FSA-Ts exhibited lower density. FSA-T10 exhibited lower thermal conductivity, surface hardness, and bulk mechanical strength as compared to FSA. However, it was found to show higher hydrophobicity as compared to that of FSA.