Trimethyloxonium tetrafluoroborate is widely used as a strong methylating agent in organic synthesis. It is particularly effective in methylating sensitive functional groups such as alcohols, amines, and carboxylic acids, where milder reagents may fail. This compound is often employed in the preparation of methyl ethers, esters, and quaternary ammonium salts. Its high reactivity makes it valuable in the synthesis of complex molecules, including pharmaceuticals and fine chemicals. Additionally, it is utilized in the methylation of nucleobases in DNA and RNA research, aiding in the study of genetic material. Its ability to function in non-aqueous environments further enhances its utility in specialized chemical reactions.