The recent advances in next-generation sequencing (NGS) has accelerated the research studying host-microbial interactions using omics-based approaches such as transcriptomics, metagenomics and metatranscriptomics. Transcriptomics analysis reveals the functional changes of host (tissue and/or cells) at molecular level under different metabolic and physiological conditions, while metagenomics and metatranscriptomics analyses capture the whole genome (DNA) and transcriptome (RNA) repertoire of the microbiome, providing both taxonomic and functional information of microbiota. In the last decade, the rumen microbiome has been widely explored to understand phylogenetic diversities and functional characteristics, especially with the advancement of molecular biological techniques. To date, hundreds to thousands of microbial phylotypes have been identified from various rumen samples via sequencing of marker gene PCR amplicons (amplicon sequencing). However, due to the lack of available genomes for many important but uncultured rumen microbiota, there is still a large gap in accurate prediction of rumen microbial functional profiles based on the existing single species genomic information. Therefore, metagenomics and metatranscriptomics represent useful tools to globally catalog microbial gene/transcript profiles that reflect overall metabolic functions of the rumen microbiota. In addition, ruminal epithelial metabolic functions including nutrient absorption, cell proliferation, and energy metabolism influence the rumen environment via altering the ruminal pH and short chain fatty acid concentrations. However, research on rumen functionality as a whole (epithelial tissue and the rumen digesta) is lacking. To gain better understanding of the rumen function, the metagenomics-, metatranscriptomics-, and transcriptomics-based research to study host-microbial interactions in the rumen will be reviewed and the pros and cons of these methods will be discussed.