Taking the rural household biogas digesters with desirable and undesirable biogas productivity in Qinghai Province as study objects, the metagenomics methods were applied to investigate the microbial community structure and the functional characteristics in the sludge samples of digesters at annual peak and nadir temperatures. Species annotation results indicated high taxon richness and biodiversity in the fermentation system. Concerning bacterial groups, Bacteroidetes, Firmicutes and Proteobacteria were the most abundant species, accounting for 72.37%~74.00% relative abundance of all floras, and they might play key roles in the fermentation. The abundance of Synergistetes (1.62%~4.73% relative abundance) in each sample was consistent with the varied biogas productivity, so the Synergistetes could be an important functional group considerably affecting biogas production. At genus level, Marinospirillum (6.75%), Clostridium (4.56%), Treponema (3.60%), and Pseudomonas (3.01%) were the dominant groups. Regarding archaeal groups, Methanogenium (25.41%~31.65% relative abundance) was the most dominant and decisive functiongroup for biogas production. Functional annotations indicated that samples from digesters with higher biogas production had more effective genes than the digesters with lower biogas production, and that the functional genes involved in methane metabolism pathways showed significantly higher abundance. The methane metabolic pathways to reduce CO2 by hydrogenotrophic methanogens were complete in all samples, and the abundance of functional enzyme genes was higher in the samples with higher biogas production. The research result indicated that H2 oxidating/CO2reducing was the major pathway for methane production in the Qinghai biogas rural fermentation system. 