Complex chromosomal rearrangements (CCRs) are often observed in clinical samples from patients with cancer and congenital diseases but are difficult to induce experimentally. For generating animal models, these CCRs must be induced as desired, because they can generate profound genome instability and/or result in cell death. This is the first study to present the establishment of an animal model for CCRs. The disruption ofRecql5, which degrades RAD51 during DNA repair, successfully induces CRISPR/Cas9-mediated CCRs, establishing a mouse model containing triple fusion genes and megabase-sized inversions. Notably, some of these structural features of individual chromosome rearrangements use template switching and microhomology-mediated break-induced replication mechanisms and are reminiscent of the newly described phenomenon chromoanasynthesis. Whole-genome sequencing (WGS) analysis revealed that the structural variants in these mice caused only target-specific rearrangements but not target-independent complex ones. Thus, these data demonstrate that CCRs can be efficiently induced by manipulating DNA repair pathways.