We demonstrate a general approach to introduce hydrophobic functional polymers into a multilayer film using the layer-by-layer (LBL) assembly method that normally works for water-soluble polyelectrolytes. To this end, two new amphiphilic diblock copolymers each containing a hydrophobic side-chain liquid crystalline polymer (SCLCP) were synthesized using atom transfer radical polymerization, followed by a modification reaction. They are poly(acrylic acid)-b-poly{6-[4-(4'-cyanophenyl)phenoxyl hexyl methacrylate} (PAA-b-PCMA) and quatrnized poly(4-vinyl pyridine-b-poly {6-[4-(4-ethyloxyohenylazo)phenoxy]hexyl methacrylate} (QP4VP-b-PAMA). We show that through the use of their micelles in aqueous solutions, which have a polycation (QP4VP-b-PAMA) or a polyanion (PAA-b-PCMA) corona, the two hydrophobic SCLCPs can be LBL assembled. The characterization results indicate that the LC phases are retained in the film, and that the SCLCPs are subjected to confinement effects inside the nanodomains defined by the core regions of the micelles. This micellar route to LBL assembly of hydrophobic functional polymers is general and offers new possibilities of designing nanostructured materials.