The fabrication of three-dimensional (3D) diamond photonic crystals with controllable nanoroughness (≤120 nm) on the surface from epoxy-functionalized cyclohexyl polyhedral oligomeric silsesquioxanes (POSS) is reported. The nanoroughness is generated on the 3D network due to microphase separation of the polymer chain segments in a nonsolvent during the rinsing step in holographic lithography process. The degree of roughness can be tuned by the crosslinking density of the polymer network, which is dependent on the loading of photoacid generators, the exposure dosage, and the choice of developer and rinsing solvent. Because the nanoroughness size is small, it does not affect the photonic band gap position of the photonic crystal in the infrared region. The combination of periodic microstructure and nanoroughness, however, offers new opportunities to realize superhydrophobicity and enhanced dye adsorption in addition to the photon management in the 3D photonic crystal.