The fermented chopped pepper in a large ceramic jar was selected as the research object， its organic acids were determined by high performance liquid chromatography， and the differences of volatile substances and microorganisms at the next three different spatial levels were analyzed by headspace solid-phase microextraction-GC-MS and high-throughput sequencing. The results showed that the organic acid and volatile matter content and microbial composition were significantly different at each spatial level (P<0.05). Among them， the content of total volatile substances was upper layer > lower layer > middle layer， and Klebsiella， Enterobacter， Tetragenococcus， Staphylococcus， etc were the dominant fermentation bacteria. The correlation analysis showed that multiple species of bacteria in the samples had a positive effect on the formation of organic acids and flavor compounds. This study revealed the differences in the fermentation of chopped peppers at the spatial level， and provided a theoretical basis for improving the quality of chopped peppers in the industrialized production.