Structural variations drive plant genome evolution and shape agronomic traits. Manipulating structural variations has great potential to improve complex plant traits and enhance agricultural sustainability. Genome editing technologies have evolved from gene knockouts and base editing to the modification of short DNA fragments, and are now advancing towards the precise manipulation of large DNA fragments. This advancement facilitates targeted, large-scale genomic changes such as deletions, insertions, replacements, inversions, translocations and duplications. In this Review, we summarize recent advances in developing technologies for large DNA fragment editing and highlight their key applications in plants as well as their potential to accelerate crop improvement. Finally, we discuss the current challenges and future prospects for these technologies in plant science.