Both yaks and Simmental are dual-purpose highland varieties, but the mechanisms behind the differences in their milk production are not yet fully understood. This study compared milk composition, rumen microbial communities, and metabolomes across a range of lactation stages for both breeds. Yak milk yields were lower and it had higher levels of fat, protein, long-chain and polyunsaturated fatty acids, key amino acids, and essential minerals than Simmental milk. The microbial community of yak rumen exhibited unique characteristics, with the Family_XIII_AD3011_group persistently enriched and positively correlated with rumen fermentation parameters and milk quality, and the content of glutamate and glutamine in yak rumen was higher than in Simmental and positively correlated with milk quality. Therefore, key microorganisms and metabolites in yak rumen are crucial factors for high-yield dairy production, providing new insights to enhance milk production in ruminant dairy cattle.