This study aimed to investigate the effects of steam-flaked corn on growth performance, serum biochemical parameters, rumen parameters, microbial community composition, species function, and metabolism in yaks using multi-omics technologies. Fourteen healthy Zhongdian yaks aged 3–4 years with similar body weights were selected and randomly divided into two groups. They were fed total mixed rations containing either ground corn (GC) or steam-flaked corn (SFC), respectively. The trial lasted for 65 days, including a 10-day adaptation period. At the end of the trial, rumen fluid samples were collected for metagenomic and metabolomic analyses. The results show that the dominant bacterial phyla in the yak rumen were Bacteroidetes and Firmicutes, and the dominant genus was Prevotella. The abundance of Fibrobacter was significantly higher in the SFC group than in the GC group . Firmicutes bacterium CAG:103 was significantly positively correlated with acetate, propionate, and butyrate, Ruminobacter sp. RM87 and Ruminobacter amylophilus were significantly positively correlated with propionate, and Butyrivibrio hungatei was significantly positively correlated with isobutyrate and isovalerate. CAZy database annotation revealed that the abundance of GH was significantly higher in the SFC group than in the GC group, while the abundances of CBM and CE were extremely significantly higher in the SFC group. Prevotella sp. CAG:1124 and Ruminococcaceae bacterium YAD3003 were significantly positively correlated with ko00500. Succinimonas amylolytica and Tolumonas lignilytica were significantly positively correlated with ko00540 (P<0.05). The rumen of yaks in the SFC group was characterized by the accumulation of purine degradation products (e.g., 3-methyladenine) and neuroactive substances (e.g., tryptamine), whereas the GC group was enriched with various bacterial fermentation products and signaling molecules, including indole-3-carboxylic acid, and showed significant enrichment in the sphingolipid metabolism pathway. Succinivibrionaceae bacterium WG-1 was significantly positively correlated with indole-3-carboxylic acid. Steam-flaked corn altered the structure and metabolism of the rumen microbial community in yaks.