A method for patterning self-assembled colloidal photonic crystals and a method for fabricating three-dimensional photonic crystal waveguides having an inverted-opal structure using the patterning method. The patterning method includes depositing first and second conductive films separate from each other, on an area corresponding to a pattern of the self-assembled colloidal photonic crystals that are to be formed on a substrate and on another area except for the area corresponding to the pattern, respectively, and growing the photonic crystals on the substrate on which the first and second conductive films are deposited by dip-coating in a fluid containing colloidal particles while applying a DC voltage to the respective first and second conductive films. Various types of colloidal photonic crystals can be fabricated depending on the electrode pattern defined on the substrate. Additionally, three-dimensional photonic crystal waveguides of an inverted-opal structure having a photonic band gap in all light-traveling directions can be fabricated.