Shanxi aged vinegar (SAV) is a well-known vinegar produced by traditional solid-state fermentation and has been used in China for thousands of years. However, how microorganisms and their metabolites change along with fermentation is unclear. Here, 454 high-throughput sequencing and denaturing gradient gel electrophoresis were used to investigate the composition of microbial community. Metabolites were further analyzed by gas chromatography-mass spectrometry and high-performance liquid chromatography. Results showed that the composition of bacterial community changed dramatically at different stages of fermentation. The bacterial genera (relative abundance > 0.1%) decreased from 17 in daqu (starter used in starch saccharification) to 2 at the 12th day of alcohol fernemtation (AF). 15 bacterial genera at the 1st day of acetic acid fermentation (AAF) decreased to 4 genera, involving Acetobacter (50.9%), Lactobacillus (47.9%), Komagataeibacter (formerly Gluconacetobacter, 0.7%) and Propionibacterium (0.1%) at the 7th day of AAF. The structure of fungal community was more homogeneous. Saccharomyces and Saccharomycopsis were predominant in AF and AAF. A total of 87 kinds of nonvolatile metabolites were detected. Canonical correspondence analysis showed a significant correlation between the microbiota succession and the formation of metabolites during the fermentation of SAV. This study provides detailed information for the fermentation mechanism of traditional SAV.