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Chromosomal fissions, fusions and whole-genome duplications propel genome evolution, yet their impact on meiotic recombination is obscured by the centromere constraint, since in monocentric species most large rearrangements are lethal. Holocentric organisms, which distribute kinetochore activity along the entire chromosome, overcome this barrier and therefore offer a unique window onto the interplay between karyotype change and crossover control. We assembled chromosome-scale genomes for 20 holocentric Rhynchospora species (including 56 haplotypes), representing all major clades of the genus, featuring satellite-based holocentromeres, and integrated single-gamete crossover maps, high-resolution meiotic synapsis cytology and Hi-C chromatin architecture. Breakpoint analysis shows that holocentromeric Tyba satellite arrays are recurrent hotspots for both chromosome fusions and fissions, contributing to the genus's extraordinary chromosome number variation from 2n = 4 to 36. Crossover landscapes group into two apparent modes: strongly distal-biased versus irregularly distributed, which is correlated with divergent patterns of synapsis elongation. Moreover, crossover number scales with chromosome count and meiotic axis length. In contrast, crossover density per megabase is inversely related to chromosome length and to chromatin-loop size. We propose that chromosome fissions create karyotypes with smaller chromosomes folded into shorter loops, thereby increasing the axial substrate accessible for double-strand break formation and elevating recombination frequency. Together, our results provide a structural link between large-scale structural chromosome evolution and meiotic recombination through coupled changes in chromosome number, size, loop geometry, and synapsis dynamics. ### Competing Interest Statement The authors have declared no competing interest.