Layer-by-layer (LbL) synthetic technique has been used to deposit multilayers composed of a wide range of materials including polymers, colloidal particles, and biomolecules. A more complex organization of nanocomponentswithin layers (intralayer) and across layers (interlayer)beyond simple deposition is required for manufacturing next-generation materials and devices. Recently, LbL was used to fabricate multilayer stacked polymer–nanocrystal nanocomposites composed of a stacking sequence of two immiscible polymer thin films. However, the requirement of two immiscible polymers limits its widespread use for the fabrication of various nanocomposites. Here, we presented a new and simplified synthetic method for the fabrication of multilayer stacked nanocomposites composed of multilayer plasmonic nanocrystal arrays stacked in a homogeneous polymer matrix via iterative sequential LbL deposition of polymer thin films and nanocrystal arrays. This novel fabrication technique requires strong attractive interaction between the “ligand shell” on the nanocrystal surface and the polymer matrix [Flory–Huggins interaction parameter of the ligand shell–polymer matrix (χ) < 0], which can dramatically enhance the stability of nanocomposites during the LbL deposition. The optical properties of plasmonic nanocomposites can be manipulated by the adjustment of the intrinsic property of the nanocrystal and/or coupling effect between adjacent nanocrystals from the same layer (intralayer) and/or the neighboring layer (interlayer). Taking advantage of this novel LbL fabrication technique, the properties of multilayer plasmonic nanocrystal arrays stacked in a homogeneous matrix can be manipulated via tuning the interlayer or intralayer coupling between nanocrystals, which can be achieved by sophisticated control of the packing density of two-dimensional nanocrystal arrays in each individual layer or the thickness of the polymer thin film between two adjacent nanocrystal arrays, respectively. These results provide a facile and effective way of designing a more complex multilayer nanostructure with controllable properties in a homogeneous polymer matrix.