Fresh burdock (Arctium lappa L.) roots were fermented with probiotic lactic acid bacteria, including Lactobacillus paracasei (L. paracasei), Lactobacillus plantarum (L. plantarum), and Lactobacillus casei (L.casei). The dynamic changes in volatile flavor compounds (VFCs) and microbial community succession were compared during fermentation. Subsequently, correlations between bacteria and characteristic VFCs were analyzed, and potential functions were predicted. The results show that the types of VFCs increased from 25 to 54, and the total content increased from 7.852 ± 1.025 to 48.325 ± 0.624 mg/kg after fermentation for 7 days. Notably, esters and alcohols increased significantly. A total of 42 VFCs were identified as contributors to the overall flavor profile of the fermented burdock root. Among these, ethyl caproate, acetaldehyde, isoamyl acetate, hexaldehyde, phenylacetaldehyde, linalool, and 3-methylbutanol were regarded as the primary characteristic VFCs. Microbial composition analysis revealed three dominant phyla, two dominant genera, and three dominant species. Among them, L. paracasei and L. plantarum were the dominant species during fermentation. L. paracasei was positively correlated with multiple characteristic VFCs and was considered the core functional species in terms of flavor formation. Notably, L. paracasei exhibited a very strong correlation with acetaldehyde (ρ = 0.99). PICRUST2 function prediction further revealed that carbohydrate metabolism and amino acid metabolism were the core pathways of microbial metabolism and important sources of flavor precursors. This study demonstrates that lactic acid bacteria fermentation could markedly improve the flavor quality of burdock roots. Moreover, the formation of VFCs was closely correlated with complex microbial metabolism during fermentation.