Syngas biomethanation is a complex process mediated by an intricate microbial consortium, which gained much attention due to its higher advantage than catalytic syngas methanation. However, there is still needing deeper conclusion on the microbial insight into the functional microbes and involved metabolic relationship. In our study, three different anaerobic inocula were applied for CO and syngas biomethanation to study the effect from the initial microbial community. The results demonstrated the microbial structure could significantly alter CO consumption and methanation rates. Genome-centric metagenomics analysis revealed that there was different CO consumer metagenome assembled genomes (MAGs) with various CO conversion pathways. Apart from the CO consumer, Coprothermobacter sp. and Methanothermobacter sp. dominated all the CO/syngas biomethanation systems, with predicted function converting generated acetate to H2/CO2 for methane generation by hydrogenotrophic methanogen. In addition, CO and syngas were used for co-fermentation with glucose, protein, and lipid. The results showed that the CO consumption rate was significantly improved via co-fermentation with organic matters. According to the genome-centric metagenomic analyses, the CO was mainly consumed in autotrophic type for acetate and H2/CO2 generation in CO solely added system. The generated acetate was further converted to H2/CO2 via a novel glycine cleavage combining partial Wood-Ljungdahl (WL) pathway for methane generation by hydrogenotrophic methanogens. The added protein promoted the growth of heterotrophic CO consumers for faster CO consumption. This study deciphered the metabolic mechanism of functional microbes, which paved pathway for efficient strategy for syngas biomethanation.