Sheep plays a vital role as ruminant animal, which contribute to human needs by supplying milk, mutton and cashmere. As lifestyle of people is improved, there is an increasing need for mutton and its products. Fungi are important component of the microbiota and may affect immune and inflammatory responses, digestion, and nutrients absorption. However, little information is available about the fungal microbiota in sheep on the plateau. Forty-five sheep were divided into five groups equally (n = 15) (AL, BL, CL, DL and EL), sheep in CL, DL and EL were given grain feeds twice daily. Sheep in AL were fed with alfalfa and oat grasses, and BL was offered with equal amount of alfalfa grass, oat grass and grain feeds. Samples of rumen fluid were collected from sheep for microbiome analysis after a four-month raising period. The microbiota analysis of collected rumen fluid samples revealed 2 333 664 filtered sequences and 3810 ASVs. Alpha diversity analysis showed obvious different chao1, Shannon_entropy and Simpson in sheep. A total of 7 phyla and 56 genera including potential beneficial fungi like Penicillium, Torula, Filobasidium, Tomentella and pathogenic Rhodotorula, etc. were significantly different in sheep. Our findings provide new insights of the diverse diets on the fungal microbiome of sheep and contribute for better feeding practices of sheep reared on the plateau.