The invention relates to a multifunctional catalyst having a nano/micro-scale reaction and separation coupling function. The multifunctional catalyst comprises a core carrier containing a catalytic hydrogenation active component, wherein a molecular sieve shell layer having shape selection or isomerization capability is formed on the core carrier; the molecular sieve shell layer is one or two of ZSM-5, Silicalite-1 or a mordenite type molecular sieve; the molecular sieve shell layer is of a cylindrical staggered intergrowth structure; and the staggered intergrowth structure grows vertically to the outer surface of the core carrier. Through adoption of the catalyst disclosed by the invention, nano/micro-scale reaction and separation coupling can be realized; the process flow of a current hydroisomerization reaction is improved; the operation cost is reduced; the production efficiency is increased, and efficient coupling of reaction and separation processes is realized. The catalyst can be applied to various hydrogenation and isomerization processes.