This study presents the first genome-wide DNA methylation landscape of the dairy cow rumen microbiome, integrating Oxford Nanopore Technologies (ONT) long-read sequencing with metagenomics and metatranscriptomics to investigate methane emission divergence. By comparing high- and low-methane-emitting Holstein cows, the research reveals that microbial DNA methylation (particularly 5mC and 6mA) is strongly associated with transcriptional regulation of key metabolic pathways, including methanogenesis and volatile fatty acid synthesis, rather than microbial taxonomic composition alone. The work establishes an epigenetic regulation-based framework that advances understanding beyond traditional species abundance models, identifying novel methylation motifs and gene-level regulatory patterns that influence carbon and hydrogen metabolic flux. This repository provides analysis scripts and pipelines used for multi-omics integration, genome-resolved metagenomic catalog construction, methylation profiling, and functional association analysis described in the study.