Liquid crystal elastomers (LCEs) are stimulus‐responsive materials with intrinsic anisotropy. However, it is still challenging to in situ program the mesogen alignment to realize three‐dimensional (3D) deformations with high‐resolution patterned structures. This work presents a feasible strategy to program the anisotropy of LCEs by using chalcone mesogens that can undergo a photoinduced cycloaddition reaction under linear polarized light. It is shown that by controlling the polarization director and the irradiation region, patterned alignment distribution in a freestanding LCE film can be created, which leads to complex and reversible 3D shape‐morphing behaviors. The work demonstrates an in situ light‐writing method to achieve sophisticated topography changes in LCEs, which has potential applications in encryption, sensors, and beyond. A programmable liquid crystal elastomer (LCE), where anisotropy can be written by linearly polarized light based on the photoinduced cycloaddition reaction of chalcone mesogens, is accomplished. Importantly, the sophisticated topography changes are realized by implanting regionally distributed anisotropy into LCE sheets.