Large-fragment genome engineering is expanding the scope of plant genome manipulation from individual genes to chromosome-scale redesign. Recent advances in double-strand break-, prime-editing-, recombinase-, and transposase-based technologies enable programmable deletion, insertion, replacement, duplication, inversion, and translocation of DNA fragments ranging from kilobases to megabases. In this review, we summarize the major strategies for large-fragment genome engineering in plants, compare their strengths and limitations, and discuss their applications in fundamental plant biology and crop breeding. We further highlight how artificial intelligence is accelerating the optimization of genome-engineering technologies, particularly through enzyme discovery, de novo protein design, protein engineering, and prediction of editing outcomes. Emerging applications include rewiring gene expression, endogenous protein tagging, targeted gene stacking, engineering genetic linkage, karyotype engineering, and multiplex genome editing. The integration of these technologies is driving a transition from genome editing to chromosome engineering, offering new opportunities for crop improvement, plant synthetic biology, and the rational design of plant genomes.