Modernized mechanization and intelligent transformation are the trends of Chinese baijiu industry development. However, these changes affect the operational environment, which lead to the decreased metabolism of esters during baijiu fermentation, especially for ethyl lactate. Ethyl lactate is an important flavor compound in most types of baijiu, which is mainly produced by esterification of lactic acid and ethanol. However, considerably less is known about the dynamic microbial succession related to ethyl lactate metabolism during the modernized baijiu fermentation process. In this study, we investigated the lactic acid bacteria, yeast and mold community succession and ethyl lactate metabolism during baijiu fermentation. Results showed that fermentation mode had a significant effect on lactic acid and ethyl lactate metabolism (p < 0.001). Specifically, the accumulation of lactic acid in modernized process was 50% lower than that in traditional process (23.22 ± 7.41 g/kg versus 33.92 ± 2.32 g/kg fermented grains). The accumulation of ethyl lactate in the modernized baijiu fermentation process (9.46 ± 1.78 g/kg fermented grains) was significantly lower than that in traditional baijiu fermentation process (37.10 ± 5.86 g/kg fermented grains). Moreover, Illumina Miseq sequencing showed 11 lactic acid bacteria OTUs, 6 yeast OTUs and 4 mold OTUs were abundant during fermentation. Compared with traditional baijiu fermentation process, modernized process led to more Lactobacillus and Candida, but less Pichia, Aspergillus, Rhizomucor and Rhizopus during fermentation. Based on the redundancy analysis and correlation network analysis, our study showed the metabolism of ethyl lactate mainly related to the activities of Pichia, Aspergillus, Rhizomucor and Rhizopus, especially for Rhizomucor and Rhizopus. This study revealed that the regulation of Pichia, Aspergillus, Rhizomucor Rhizopus and Candida might be an effective orientation for adjusting the metabolism of ethyl lactate during modernized baijiu fermentation.