A novel technique was proposed to fabricate a three-dimensional photonic crystal by self-assembling microspheres and the autocloning technology. The autocloning thin-film layers were superimposed on the prepared two-dimensional structural substrates using self-assembled microspheres. The thin-film process allows the three-dimensional periodic structure to be easily modified in the thickness dimension to structure as needed. We analyzed the etching effect using the unified process model according to the surface movement and surface velocity of the film to achieve the surface profile of the SiO2 adjusting layer. Finally, 17 layers of Ta2O5/SiO 2 multilayers were stacked on the SiO2 adjusting layer successfully.