This paper describes a facile method for the fabrication of photonic crystal heterostructures (PCHSs) composed of photonic crystals (PCs) of core-shell spheres with different diameters and effective refractive indexes. The PCs are fabricated by a simple vertical deposition technique. The PCs of monodisperse polystyrene/silica core-shell (PS@SiO2) spheres or hollow silica spheres are used as substrates to fabricate PCHSs, respectively. The results indicate that the resultant PCHSs formed from PS@SiO2 spheres or hollow silica spheres have a very high quality and a good adsorbing interface between the PCs. Transmission spectra show that there are two optical stop bands of the PCHSs, and the positions of optical stop bands are controlled by tuning the size and the effective refractive index of spheres. The PCHSs formed from hollow silica spheres may facilitate the development of the potential applications due to the novel properties of hollow silica spheres, such as, low density, low refractive index, and high specific surface area.