Objective To explore the cross-border enhancement effect of Huniang 3.042 in Baijiu brewing.Methods One percent of Huniang 3.042 seed culture is inoculated into the traditional medium-high temperature Daqu raw materials for fortified Daqu production and fermentation with refermentation grains. Then, with the Daqu and the crude Baijiu fermented by refermentation grains as samples, the physicochemical properties and microbial community composition of the Daqu, as well as the correlation between the flavor compounds in the crude Baijiu and the primary microorganisms in the Daqu are analyzed using single-molecule real-time sequencing (SMRT) and headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS).Results ① The fortified Daqu exhibits slightly decreased water content (P>0.05), significantly decreased acidity (P<0.05), slightly increased liquefaction power (P>0.05), as well as significantly increased protease, saccharification power, fermentation power, and esterification power (P<0.05). ② The fortified Daqu shows decreased bacterial diversity and increased fungal diversity, with 6 dominant microbial genera of Bacillus, Lederbergia, Heyndrickxia, Cronobacter, Thermoascus, and Aspergillus. ③ Compared with the control group, the crude Baijiu of the fortified Daqu group demonstrates a small difference in flavor compound types (P>0.05), increased total amount of flavor compounds by 22.19% (P>0.05), including ketones increased by 81.32% (P<0.05) and pyrazines by 360.26% (P<0.01), slightly increased esters and aldehydes, as well as slightly decreased alcohols (all P>0.05). Furthermore, 20 key differential compounds are determined (P<0.05, VIP>1), mainly presenting fruity, floral, creamy, and roasted aromas. ④ Aspergillus and Bacillus are positively correlated with ethyl methyl butyrate (P<0.05), while they are positively correlated with pyrazine and ketone compounds.Conclusion Fortification with 1% Huniang 3.042, medium-high temperature Daqu demonstrates improved physicochemical properties and microbial structures, thereby increasing key flavor compound content in Li Du crude Baijiu.