Soil water repellency (SWR) is a physical phenomenon whereby water cannot penetrate or has difficulty penetrating the soil surface. There are many factors involved in its occurrence, but the main factors controlling its emergence in loess remain unclear. In this work, we have studied numerous physicochemical and biological factors functioning in different dominant vegetations ( Carr., L., and L.) in a loess hilly region by gas chromatography-mass spectrometry (GC-MS) and high-throughput sequencing techniques. We observed that more than 75% of the soils under and are categorized as slightly or strongly water repellent, while nearly 50% of the soils under are categorized as severely to extremely water repellent. The relative concentrations of total free lipids in the soil in the same water-repellency class were > > , where fatty acids, alkanols, and sterols were positively correlated with SWR, whereas alkanes were not. For the abundance and diversity index of bacterial and fungal communities, the three species ranked in the following order: ≈ > . Thus, solvent-extractable polar waxes were indicated to be better preserved in water-repellent soils under due to lower microbial diversity than and . Here, we demonstrate polar waxes to be the principal factor controlling SWR. Moreover, the dominant phyla of fungi varied greatly than those of bacteria under three vegetation types. Correlation analysis showed that the abundance of in dominant bacteria increased with SWR. Nonmetric multidimensional scaling suggested the fungal community in different water-repellent soils under to vary more than those under and . The indicator species mainly belonged to in bacteria and in fungi at the phylum level; this finding was further supported by the linear discriminant analysis (LDA) effect size (LEfSe). Additionally, GC-MS identified a small amount of ergosterol, a specific biomarker of fungi under . These pieces of evidence collectively reveal that severe to extreme SWR occurs under and appears to be the most influenced by fungi and actinomycetes when the topsoil is close to air drying. However, there is a need for further testing on different plant species or land use.