Hierarchical architecture is of vital importance in soft materials. Focal conic domains (FCDs) of smectic liquid crystals, characterized by an ordered lamellar structure, attract intensive attention. Simultaneously tailoring the geometry and clustering characteristics of FCDs remains a challenge. Here, the 3D smectic layer origami via a 2D preprogrammed photoalignment film is accomplished. Full control of hierarchical superstructures is demonstrated, including the domain size, shape, and orientation, and the lattice symmetry of fragmented toric FCDs. The unique symmetry breaking of resultant superstructures combined with the optical anisotropy of the liquid crystals induces an intriguing polarization‐dependent diffraction. This work broadens the scientific understanding of self‐assembled soft materials and may inspire new opportunities for advanced functional materials and devices. Full control of 3D smectic layer origami is realized by a 2D preprogrammed photoalignment film, including both the geometry and clustering characteristics of fragmented focal conic domains (FCDs). The unique symmetry breaking of FCDs combined with the optical anisotropy of liquid crystals induces a metasurface‐like polarization‐dependent diffraction. This work broadens the scientific understanding and inspires new opportunities to soft materials.