Goose meat is consumed by consumers because it contains a relatively high proportion of polyunsaturated fatty acids (PUFAs). This study was conducted to explore the main differences in production performance, breast meat quality traits, and cecal microbiota compositions between the Zi goose (ZG) and Xianghai flying goose (FG). The production performance and breast meat quality trait analyses showed that compared with the ZG, the FG had a higher right breast muscle index, ileum villi height/crypt depth ratio (VH/CD), and cecum fermentation rate (higher short-chain fatty acid (SFCA) concentration); a lower abdominal fat index; a higher proportion of PUFAs; and a lower shear force. Spearman’s correlation coefficients between the cecal microbiota composition and production performance indexes suggested that the genus Faecalibacterium was positively associated with production performance; in contrast, the genus Candidatus Saccharimonas was negatively correlated with production performance; moreover, the Ruminococcus torques group, Parasutterella, and Methanobrevibacter were negatively related to the VH/CD. Taken together, in this particular trial, FG had better production performance, healthier meat quality traits, and better intestinal digestion and absorption capacities than ZG. These results not only provide a useful data reference for the production of healthy geese for human consumption but can also help guide the utilization of goose breed resources.