An object of the present invention is to provide a three-dimensional photonic crystal which allows an internal formation of a defect structure with an arbitrary shape and size. Multiple holes extending to two different directions are formed obliquely to a base body surface in order to form a first crystal and a second crystal. Base body left between the holes are made to be rods. Moreover, a connection crystal layer is formed by a part of rods having a size different from that of the rods in the first crystal and the second crystal. The connection crystal layer is held between the first crystal and the second crystal and they are fused. In a three-dimensional photonic crystal thus obtained, the rod becomes a point defect. The shape and size of the point defect can be arbitrarily set in any directions within the connection crystal layer. The shape and size of the point defect can also be controlled by adjusting the thickness of the connection crystal layer.