Methyl chlorooxoacetate is primarily used as an intermediate in organic synthesis, particularly in the production of pharmaceuticals and agrochemicals. It serves as a key building block for the synthesis of various active compounds, including herbicides, fungicides, and insecticides. Additionally, it is utilized in the preparation of fine chemicals and specialty chemicals, where its reactive carbonyl and chloro groups enable versatile transformations. In research and development, it is often employed in the creation of complex molecules due to its ability to participate in condensation, esterification, and nucleophilic substitution reactions. Its applications also extend to the synthesis of heterocyclic compounds, which are important in medicinal chemistry.