To provide an apparatus and method of manufacturing a photonic crystal without requiring intricate constitution and manufacturing a waveguide in the photonic crystal.

A substrate 10 containing a material which gives rise to a change in refractive index by irradiating the material with light of a specific wavelength is first prepared in the method of manufacturing the two-dimensional photonic crystal. A diffraction grating 24 is arranged to face the substrate 10. The substrate 10 is irradiated with the light (for example, UV rays) 26 of the specific wavelength through the diffraction grating 24 in this state, by which the refractive index changing sections are formed like a grid apart prescribed intervals in the substrate 10 and the photonic crystal 10' is obtained.