Milk from dairy cows is an essential nutrient for the young and human as well. Forage plays a vital role in dairy husbandry via affecting milk quality and quantity. However, the differences in mammary metabolism of dairy cows fed different forages remains elucidated. In this study, we utilized transcriptomic RNA-seq and iTRAQ proteomic techniques to investigate and integrate the differences of molecular pathways and biological processes in the mammary gland of dairy cows fed differing forages. Bovine mammary tissues were obtained from 6 healthy multiparous lactating dairy cows fed with corn stover (CS, low-quality; n = 6) and alfalfa hay (AH, high-quality; n = 6), respectively. A total of 1631 differentially expressed transcripts (DETs; 1046 upregulated and 585 downregulated) and 346 differentially expressed proteins (DEPs; 138 increased and 208 decreased) were detected in the mammary glands between the CS- and AH-fed animals. Expression patterns of 33 DEPs (18 increased and 15 decreased) were consistent with the expression of their mRNAs. The gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses of the DETs and DEPs indicated that the decreased energy metabolism, increased fatty-acid oxidation, attenuated protein synthesis, enhanced protein degradation, and the lower mammary cell growth may be the prime factors contributing to the lower milk production in the CS-fed cows compared with the AH-fed cows. Moreover, 19 milk-synthesis-related genes were quantitated by real-time RT-PCR to examine the transcriptional profile and validate the proteins identified by LC-MS/MS between CS-fed and AH-fed bovine mammary gland. Four DEPs were further verified by Western blot analysis. These results provide the biological understanding of insights into mammary metabolism alterations affected by differing foraged and will be beneficial in developing highly efficient strategies for utilization of low-quality forages.