Chinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, whileGeotrichum silvicola,Torulaspora delbrueckii,Hanseniaspora uvarum,Saturnispora silvae,Issatchenkia orientalis,Candida mucifera,Kazachstania barnettii,Cyberlindnera jadinii,Hanseniasporaspp.,Alternaria tenuissima, Cryptococcus laurentii,Metschnikowia spp., andRhodotorula dairenensiswere detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification ofSchizosaccharomyces pombeandDebaryomyces hanseniiin these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13568-023-01562-7.