Photonic crystals are utilized in many noteworthy applications like optical communications, light flow control, and quantum optics. Photonic crystal with nanoscale structure is important for the manipulation of light propagation in visible and near-infrared range. Herein, we propose a novel multi beam lithography method to fabricate photonic crystal with nanoscale structure without cracking. Using multi-beam ultrafast laser processing and etching, parallel channels with subwavelength gap are obtained in yttrium aluminum garnet crystal. Combining optical simulation based on Debye diffraction, we experimentally show the gap width of parallel channels can be controlled at nanoscale by changing phase holograms. With the superimposed phase hologram designing, functional structures of complicated channel arrays distribution can be created in crystal. Optical gratings of different periods are fabricated, which can diffract incident light in particular ways. This approach can efficiently manufacture nanostructures with controllable gap, and offer an alternative to the fabrication of complex photonic crystal for integrated photonics applications.