[Background] Yeasts are the most important microbes in Maotai-flavor Baijiu production. However, the structures and functions of core yeasts in the fermentation microbiota are unclear. [Objective] To reveal the fermentation mechanism of the Baijiu-making process and improve the product quality, we illustrated the structures and functions of core yeasts in fermentation microbiota. [Methods] Culture-independent (internal transcribed spacer amplicons and metatranscriptomics sequencing) and culture-dependent (strain selection and simulated fermentation experiments) technologies were used to analyze the structural change of yeast microbiota and function of core yeasts in the fermentation process of Maotai-flavor Baijiu production. [Results] Results of amplicons and metatranscriptomics showed that yeast in the fermentation process classified to 10 genera. We selected 13 core structure species (relative abundance>0.2%) of yeast microbiota and identified 2 core yeasts including Pichia kudriavzevii and Schizosaccharomyces pombe. In the fermentation process, the relative abundance of P. kudriavzevii had more than 89% of the total microbes in the yeast microbiota. Meanwhile, Schi. pombe expressed more than 21% of the total functional genes in the yeast microbiota. Moreover, the results of the simulated fermentation experiments showed that P. kudriavzevii could tolerate lactic acid accumulation and Schi. pombe could tolerate ethanol accumulation in the yeast microbiota. The effects of two core yeasts ensure the stability of Baijiu production during the fermentation process. [Conclusion] P. kudriavzevii and Schi. pombe are the dominant yeasts in the fermentation process of Maotai-flavor Baijiu production. These two yeasts play different roles during fermentation. Our research further deepened our knowledge about the contribution of core yeasts for fermentation process. It also makes researchers recognize the importance of the regulation of core microbes during Baijiu production.