Methane is one of the greenhouse gases. Methanogens can produce methane by metabolites of rumen microorganisms such as fungi and ciliates, that is, and the emission of methane in the process of culture is closely related to rumen microbial community. In this study, high-throughput sequencing technology was used to investigate the methanogen, ciliate and fungi communities and associations among methanogen and ciliate or fungi based on the abundances of genera and species. The results showed that Methanobacteriales and Cyclotrichida are dominant order of methanogen and ciliate respectively, and Neocallimastigomycota and Ascomycota are dominant phylum of fungi. In this study, we observed significant positive correlation between methanogens and ciliates, as well as positive and negative correlation between fungi and ciliates observed. Our results suggest that community structure of methanogens and fungi of Tashkurgan sheep rumen is consistent with other studies and ciliate community structure is different from other studies. Associations among methanogen and ciliate or fungi is related to the fermentation principle of methanogen, but it need to previous study that the mechanism of the correlation of between methanogen with fungi and ciliate identified in this study.