Abstract: Illumina NovaSeq high-throughput sequencing technology was used to sequence the fungi gene ITS2 regions of yak yogurt samples in the Gannan pastoral area, OTU clustering, alpha diversity, and beta diversity were analyzed. Through analyzing and comparing the fungal composition and diversity of yak yogurt collected at different preservation temperatures in the Gannan pastoral area, the results showed that the main fungal in yak yogurt in Gannan pastoral area was Ascomycota at the phylum level, the abundance value was 82.09%~99.25%; at the genus level, among which Saccharomyces was the dominant with the abundance value was 23.98%~63.49%, followed by Kluyveromyces with the abundance value 16.08%~31.89%, Pichia with the abundance value 3.39%~35.21%. There was no significant difference in fungal diversity among yak yogurt samples which were collected at four different preservation temperatures in the Gannan pastoral area, the fungal community composition of the sampling groups was similar at all levels of classification, with only some differences in composition ratio.