Abstract: Wine flavor and quality are highly dependent on the synergistic interactions between microbial communities. This review systematically summarizes recent advances in breeding technologies employed to optimize core wine microorganisms (primarily yeasts and lactic acid bacteria). Among these techniques, hybrid breeding can integrate desirable traits of the parental yeast strains. Yeasts generated using hybrid breeding showe enhanced fermentation efficiency and promote ester synthesis compared to the parent strains. Genetic engineering and metabolic engineering enable precise regulation of yeast metabolic pathways, making them possible to successfully increase the yields of key flavor compounds. Furthermore, adaptive laboratory evolution is employed to enhance the stress resistance of yeast and lactic acid bacteria strains in the winemaking environment. However, the application of these technologies still faces challenges, such as insufficient genetic and fermentation stability of cross-species hybrid/fused strains, potential off-target risks in gene editing, and regulatory restrictions. Future research needs to focus on developing multi-technology integrated strategies and strengthening research on the construction of artificial microbial communities and marker-free gene editing technologies to promote winemaking towards greater efficiency, safety, and precise flavor regulation.