1,3-Dithiane is widely used as a protective group in organic synthesis, particularly for carbonyl compounds. It forms stable cyclic thioacetals with aldehydes and ketones, shielding them from reactive conditions during complex chemical transformations. This property makes it valuable in multi-step synthesis, where selective protection and deprotection are required.

In addition, 1,3-dithiane serves as a key reagent in the Corey-Seebach reaction, where it acts as a masked acyl anion equivalent. This allows for the introduction of carbon chains or functional groups into molecules, making it a versatile tool in the construction of complex organic structures.

It is also employed in the synthesis of pharmaceuticals, agrochemicals, and natural products, where its ability to stabilize intermediates and facilitate selective reactions is highly advantageous. Furthermore, 1,3-dithiane derivatives are explored in materials science for their potential in creating sulfur-containing polymers and advanced materials.