High-quality three-dimensional photonic crystal (PC) heterostructures were fabricated using the modified self-assembly method, and their structural and optical properties were analyzed. Results suggest that the optical quality of heterostructures formed by depositing bigger particles on small ones is superior to that of heterostructures formed by stacking smaller particles on big ones, due to the rough interface effects in the latter structure. The roughness of the interface in the latter structure can be largely improved by introducing a thin two-dimensional planar defect layer into the PCs, and significant progress in the quality of the heterostructures is achieved. The important role of the thin planar defect layer in the quality of the heterostructures was also verified by numerical simulations.