Light-struck taste rice wine (LST-RW) is the most popular new rice wine at present, which is brewed by a variety of microorganisms. However, the relationship between microorganisms and flavor substances in light-struck taste rice wine is still unexplored. In this study, high-throughput sequencing, high-performance liquid chromatography (HPLC), headspace solid-phase microextraction (HS-SPME), and gas chromatography–mass spectrometry (GC–MS) were used to prove that microbial community had significant influence on flavor substances during light-struck taste rice wine fermentation. The results indicated a consistent increase in the majority of amino acids and organic acids within LST-RW with extended fermentation duration. A total of 49 volatile flavor compounds, including alcohols, esters, and aldehydes, were identified. In the brewing process of LST-RW, Bacillus (17.13 %) and Saccharopolyspora (15.55 %) emerge as the predominant bacterial genera; Aspergillus (83.34 %) and Saccharomyces (15.21 %) emerged as the dominant fungal genera. A notable correlation was observed between fermentation microorganisms and flavor substances. Microorganism species exhibiting strong co-exclusion or symbiotic relationships were also identified. The research findings offer a theoretical reference for optimizing and innovating the fermentation process of LST-RW.