In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high-and low-quality diets. In total, 340, 338, 337, 330, and 328 miRNAs were expressed in the rumen, duodenum, jejunum, liver, and mammary gland tissues, respectively. Some miRNAs were highly correlated with feed and nitrogen efficiency, with target genes involved in transportation and phosphorylation of amino acid (AA). Additionally, low-quality forage diets (corn stover and rice straw) influenced the expression of feed and nitrogen efficiency-associated miRNAs such as miR-99b in rumen, miR-2336 in duodenum, miR-652 in jejunum, miR-1 in liver, and miR-181a in mammary gland. Ruminal miR-21-3p and liver miR-2285f were predicted to regulate AA transportation by targeting ATP1A2 and SLC7A8, respectively. Furthermore, bovine-specific miRNAs regulated the proliferation and morphology of rumen epithelium, as well as the metabolism of liver lipids and branched-chain AAs, revealing bovine-specific mechanisms. Our results suggest that miRNAs expressed in these five tissues play roles in regulating transportation of AA for downstream milk production, which is an important mechanism that may be associated with low milk protein under lowquality forage feed.Enhancing the protein content in milk is essential for improvement of milk quality in developing countries, especially under a lack of high-quality forage. Milk protein has been considered one of the best protein sources for humans 1 , especially whey protein, whose amino acids (AA) and associated compounds can provide nutrition and bioactive substrates for humans 2 . With the improvement of Chinese quality of life, total milk production has continuously increased, leading to the rapid development of the Chinese dairy industry, which has increased 12.8% annually on average since 2000 [3][4][5] . However, in China, milk production per cow is relatively low compared with that in the developed counties such as the USA 6 . The poor milk quality has been a huge concern due to its low nutrient content, especially protein 7 . Nitrogen (N) metabolism can directly impact milk protein yield and quality. N efficiency, the ratio of milk protein yield to crude protein intake, has been considered a key regulator for milk protein synthesis 8 . When N efficiency is low, a large proportion of N will be excreted through urine, reducing the N flow to the mammary gland for milk protein synthesis 9 . Therefore, N efficiency can also be estimated by measuring the content of milk urea N (MUN), with a lower MUN content representing higher N efficiency 10 . Feed efficiency, the ratio of milk production to dry matter intake, is also an important trait that indicates the efficiency of grocery nutrients transferred to the milk of dairy cows 11 . Therefore, lower feed and N efficiency can not only decrease the nutrients enriched in the milk but also increase the energy waste...