Precise manipulation of large DNA fragments in eukaryotic genomes remains limited by the low efficiency and delivery constraints of current multicomponent editing systems. In this study, we engineered an RNA-guided bridge recombinase system through rational mutagenesis and AI-assisted directed evolution, enabling programmable chromosomal rearrangements in both plant and mammalian cells and achieving up to a 29.8-fold increase in activity. In plants, the optimized system mediated precise deletions, insertions, and inversions from 1.8- to 315-kb DNA fragments, with stable editing efficiencies of up to 23.9% in regenerated rice plants. We further generated herbicide-resistant rice through a 315-kb chromosomal inversion that rewired endogenous promoter activity. In mammalian cells, the compact ISCro4 recombinase system was delivered using a single adeno-associated virus vector, thereby supporting efficient genome editing. Together, these results establish bridge RNA-guided recombinases as a versatile platform for programmable chromosome-scale genome engineering, with broad potential for precision breeding and gene therapy.