Methyl 2-chloro-6-iodobenzoate is primarily used as an intermediate in organic synthesis. It serves as a key building block in the preparation of more complex molecules, particularly in pharmaceutical research. The compound is often employed in the development of active pharmaceutical ingredients (APIs) due to its reactive sites, which allow for further functionalization. Additionally, it is utilized in the synthesis of agrochemicals, where it contributes to the creation of compounds with potential pesticidal or herbicidal properties. Its structure makes it valuable in cross-coupling reactions, such as Suzuki or Sonogashira couplings, which are essential in constructing biologically active molecules.