The purpose of this study was to reveal the relationship between core microorganisms and flavor substances in the fermentation process of corn wine. Microbial diversity, volatile and non-volatile flavor substances were detected by high-throughput sequencing (HTS), headspace solid phase micro-extraction gas chromatography-mass spectrometry (HS-SPME/GC–MS) and gas chromatography time of flight mass spectrometry (GC-TOF-MS). High performance liquid chromatography (HPLC) was used to detect organic acids in corn wine fermentation, and its physiochemical properties were tracked. The results showed that physiochemical factors changed obviously with fermentation time. Bacillus, Prevotella_9, Acinetobacter and Gluconobacter were the predominant bacterial. Rhizopus and Saccharomyces were the dominant fungi. Acetic acid and succinic acid were important organic acids in corn wine. According to variable importance of projection (VIP) > 1 and P < 0.05, 24 volatile flavor substances with significant difference were screened out from 52 volatile flavor substances. Similarly, 25 non-volatile flavor substances with significant differences were screened out from the 97 reliable metabolites identified by 223 chromatographic peaks. Eight key metabolic pathways were enriched from 25 non-volatile flavor substances according to path influence values > 0.1 and P < 0.05. Based on Two-way Orthogonal Partial Least Squares (O2PLS) model and Pearson correlation coefficient, Saccharomyces, Rhizopus, uncultured_bacterium, Aneurinibacillus, Wickerhamomyces and Gluconobacter may be the potential volatile flavor-contributing microorganism genus in corn wine. The Pearson correlation coefficient showed that Saccharomyces was significantly positively correlated with malic acid, oxalic acid, valine and isoleucine, and Rhizopus was positively correlated with glucose-1-phosphate and alanine. These findings enhanced our understanding of the formation mechanism of flavor substances in corn wine and provided the theoretical basis for stabilizing flavor quality of corn wine.