Methoxyamine hydrochloride is widely used in organic synthesis as a protecting group for aldehydes and ketones. It reacts with carbonyl compounds to form oximes, which are stable under various reaction conditions, allowing further transformations on the molecule without affecting the carbonyl group.

In pharmaceutical research, it serves as a key reagent in the synthesis of heterocyclic compounds, which are essential structures in many drugs. It is also utilized in the preparation of nucleoside analogs, playing a crucial role in the development of antiviral and anticancer agents.

Additionally, methoxyamine hydrochloride is employed in biochemical studies to modify DNA and RNA. It reacts with abasic sites in nucleic acids, aiding in the study of DNA damage and repair mechanisms. This application is particularly valuable in understanding genetic mutations and developing therapeutic strategies.

In material science, it is used in the synthesis of polymers and coatings, where its reactivity with carbonyl groups helps create specialized materials with desired properties. Overall, its versatility makes it a valuable compound in both industrial and academic research.