Composite nanomaterials are attractive for many applications including catalysis, plasmonics, sensing, imaging, and biology. In such composite nanomaterials, it is desired, yet still challenging to have a controlled alignment at the interfaces between materials with lattice parameters in disparate scales. To address this challenge, we develop a new strategy of colloidal synthesis, in which self-assembled molecular layers are introduced to control the alignment between different materials. To demonstrate this concept, self-assembled cetyltrimethylammonium bromide (CTAB) self-assembled molecular layer is used to bridge interfaces in a core-shell nanocomposite with a well-defined metal nanocrystal core and a metal-organic-framework (MOF) shell, which differs in structural dimensions by orders of magnitude. We show that single metal nanocrystals are encased individually in single-crystalline MOFs and a controlled alignment between the crystal planes of the metal and MOF is observed.