A diurnal asymmetric warming (CK: control; DW: daytime warming; NW: nighttime warming; DW+NW: daily warming) was conducted in an alpine agricultural system of the Tibet to investigate the effect of diurnal asymmetric warming on soil fungal diversity. Soil fungal community in May and August in 2017 was determined by the high-throughput sequencing. The 'NW' rather than the 'DW' and 'DW+NW' significantly increased the abundance-based coverage estimator (ACE), Chao1 and species richness at the 0–10 cm but not the 10–20 cm depth in May and August, 2017. However, the 'DW', 'NW' and 'DW+NW' did not significantly affect phylogenetic and functional α-diversity, species, phylogenic and functional composition. The straw yield of highland barley was correlated with soil fungal diversity. Therefore, daytime and nighttime warming may have different effects on soil fungal diversity, and their effects are not additive. Different dimensions diversity of soil fungal community may have different responses to climate warming. Diurnal asymmetrical warming should be considered in future agricultural managements in alpine regions under asymmetrical warming.