1,3-Enynes are a class of organic molecules with both alkyl and alkenyl groups, which have unique structural properties and have been used as the basic units in a variety of reactions to obtain a variety of specialized molecular structures. Selective difunctionalization of 1,3-enynes is an attractive strategy for the construction of 1,3-diene-type compounds, alkyne-based compounds, aromatic heterocycles such as thiophenes and pyrroles, as well as multisubstituted allene derivatives. In recent years, various catalytic strategies for the difunctionalization of 1,3-enynes have been widely reported, however, challenges in controlling the chemo- and regioselective difunctionalization of 1,3-enynes persist. The 1,2-, 3,4-, and 1,4-difunctionalization reactions of 1,3-enynes in the last few years are summarized, and the directions of development in this field are prospected.