Background: Heat stress is a key issue of growing concern for livestock industry worldwide due to its negative effects not only on milk production, fertility, health, welfare, and economic returns of dairy cows, but also on the microbial communities in the rumen. However, the underlying relationship between rumen microbiome and its associated metabolism with heat tolerance in cow have not been extensively described yet. Therefore, the main objective of this study was to investigate differential heat resistance in Holstein cows using rumen microbiome and metabolome analyses.Methods: We performed both principal component analysis and membership function analysis to select 7 heat-tolerant (HT) and 7 heat-sensitive (HS) cows. The ruminal fluid samples of two groups were collected at two hours post feeding on 7th day of heat stress period, for analyses including rumen fermentation parameters, rumen microbiome and nontargeted metabolomics.Results: Under heat stress conditions, the HT cows had a significantly higher propionic acid content than the HS cows; whereas measures of the respiratory rate (RR), rectal temperature (RT), acetic,butyric acid and acetic acid to propionic acid ratio (A:P) in the HT cows were lower compared with the HS cows. Omics sequencing revealed that the relative abundance of Rikenellaceae_RC9_gut_group, Succiniclasticum, Ruminococcaceae_NK4A214_group and Christensenellaceae_R-7_group were significantly higher in the HT than HS cows; whereas Prevotella_1, Ruminococcaceae_UCG-014, and Shuttleworthia were significantly higher in the HS cows compared to HT cows. Substances mainly involved in carbohydrate metabolism, including glycerol, mannitol, and maltose, showed significantly higher content in the HT cows compared to that in the HS cows. Simultaneously, RR was significantly correlated with both differential microorganisms and distinct metabolites, suggesting three metabolites could be potential biomarkers for determining heat resistance that require further research.Conclusion: Overall, distinct changes in the rumen microbiome and metabolomics in the HT cows may be associated with better adaptability to heat stress. These findings suggest their use as diagnostic tools of heat tolerance in dairy cattle breeding schemes.