Polymicrobial co-fermentation is among the distinct character of high-temperature Daqu. However, fungal communities in the three types of high-temperature Daqu, namely, white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, are yet to be characterized. In this study, the fungal diversity, taste, and aroma profiles in the three types of high-temperature Daqu were investigated by Illumina MiSeq high-throughput sequencing, electronic tongue, and electronic nose, respectively. Ascomycota and Basidiomycota were detected as the absolute dominant fungal phylum in all types of high-temperature Daqu samples, whereas Thermomyces, Thermoascus, Aspergillus, Rasamsonia, Byssochlamys, and Trichomonascus were identified as the dominant fungal genera. The fungal communities of the three types of high-temperature Daqu differed significantly (p < 0.05), and Thermomyces, Thermoascus, and Monascus could serve as the biomarkers in white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, respectively. The three types of high-temperature Daqu had an extremely significant difference (p < 0.01) in flavor: white high-temperature Daqu was characterized by sourness, bitterness, astringency, richness, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds; black high-temperature Daqu was characterized by aftertaste-A, aftertaste-B, methane-aliph, hydrogen, and aromatic compounds; and yellow high-temperature Daqu was characterized by saltiness, umami, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds. The fungal communities in the three types of high-temperature Daqu were significantly correlated with taste but not with aroma, and the aroma of high-temperature Daqu was mainly influenced by the dominant fungal genera including Trichomonascus, Aspergillus, Thermoascus, and Thermomyces. The result of the present study enriched and refined our knowledge of high-temperature Daqu, which had positive implications for the development of traditional brewing technique.