Reducing rumen methane emissions based on the basal diet is one primary approach for livestock production. However, microbiological mechanisms of rumen methane emissions under different diets are very complex and lack comprehensive understanding. This research developed an innovative multilayer network framework to investigate relationships of rumen microbes, transformations of metabolites and functions of rumen microbial genes. The multilayer network model explored the diets-based variation in rumen microbial system differences. The topological structure of the multilayer network reflects volatile fatty acid (VFA) fermentation characteristics between diets. Propionate is the highest degree node of the concentrate-diet (CONC) multilayer network while acetate has the highest degree in the forage-diet (FOR) multilayer network. The microbial communities under FOR diet are more diverse and have more complicated interactions. Methanobrevibacter copresented with Methanosphaera only in the CONC network. There are 33 microbial functional genes in the FOR network that are enriched in the methane synthesize functional module, including the CO2 reduction and the enzymatic reaction of acetyl phosphate to synthesize acetyl-CoA. The microbial genes of the CONC network are found to be associated with the serine biosynthetic and the biochemical process of acetate convert to acetyl-CoA and acetyl phosphate. This study verified the variations of diet-based methane phenotypic are results of systemic changing in the metabolism of the entire rumen microbiome.