Biopolymers are developed as functional intermediate linkers for the assembly of nano and submicron-sized crystals. Mediated by the interlayers, iron oxide and zeolite crystals with varied shapes (cubic, ellipsoidal, and discoidal) are organized into uniformly oriented monolayers on glass plates and macroporous alumina supports. The crystal monolayers can be near-perfect transferred onto the substrate upon calcination, which are suitable for further growth. The assembled crystals display a range of colors, and important mechanisms with direct evidence for explaining this optical appearance are proposed.