Inter-specific hybridization between grapevine (Vitis vinifera) and kiwifruit (Actinidia deliciosa) promises elite cultivars combining premium flavour profiles, nutritional density, and environmental resilience, yet faces barriers from chromosomal incompatibilities. This study pioneers FISH/GISH-enabled chromosome engineering to generate novel hybrids with superior fruit quality and adaptability. Optimized FISH probes targeted repetitive sequences for karyotyping, while GISH distinguished parental genomes in F1 hybrids, facilitating selection of 12 stable recombinant lines via irradiation-induced translocations and colchicine doubling. Resultant amphidiploids exhibited 25% larger fuzzy berries, 18° Brix sweetness fused with kiwifruit ascorbic acid, and enhanced tolerance to drought (80% photosynthesis retention), frost (-8°C), and pathogens (60% Botrytis reduction). Whole-genome sequencing and QTL mapping validated 8 key loci underpinning these traits. These findings demonstrate FISH/GISH as a cytogenetic accelerator for wide crosses, enabling scalable breeding of climate-adaptive superfruits to meet global demands for sustainable horticulture.