Liquid crystal elastomers (LCEs), as a kind of programmable, multi-stimulus responsive, reversibly deformable polymerized soft matter material, currently show great prospects in the fields of soft robots, soft actuators, flexible electronics, artificial muscles, and soft photonic devices. The multifunctional actuations of LCEs are mainly based on the complex multiplex deformations, which are induced by programmable molecular alignments. The realization of high-resolution molecular alignments of LCEs within different thickness systems has advanced requirements for the mesogen alignment technique. In this review article, we discuss the current mesogen alignment techniques and the complex multiplex deformations of LCEs within different morphology systems based on various alignment techniques. We further summarize the advances of LCEs in soft robots, tunable optical devices, smart fabrics and other fields based on programmable complex deformation, and outline the current challenges and future development trends of LCEs.