Paocai is a traditional Chinese fermented vegetable product popular in Asian countries. As an important additive, salt concentration is closely related to the quality of paocai. The aim of this study was to investigate the effect of salt concentration on the physicochemical characteristics, microbial diversity, and flavor profiles of spontaneously fermented radish, and the cross-correlation between microorganisms and flavor compounds was also revealed. Analysis of the microbial diversity of paocai showed that Firmicutes, Proteobacteria, and Ascomycota were detected as the main phyla with different salt concentrations, Weissella and Lactobacillus were the predominant bacterial genera, and Yarrowia dominated the fungal genera. Based on LEfSe analysis, Lactobacillus, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Microbacterium, Lactococcus, Staphylococcus, and Weissella were regarded as differential genera caused by differences in salinity. Analysis of the flavor compounds showed that 17 free amino acids, 5 isothiocyanates, 3 terpenes, 15 sulphur-containing compounds, 16 esters, 8 organic acids, 9 aldehydes, 8 ketones, 25 alcohols, 7 nitriles, 2 lactones, and 10 hydrocarbons were detected. Then, the correlation between the microbial community and flavor compounds was revealed, and the results indicated that several bacterial genera significantly correlated with flavors, including Lactobacillus, Kosakonia, Weissella, Leuconostoc, and Staphylococcus, while fungi had weak correlations with flavors. In addition, Metacyc pathway analysis was carried out to elucidate the effect of salt content on the metabolic pathways, showing that most flavor-related pathways were up-regulated with the increase in salt content. Results presented in this study may contribute to further understanding the role of salt in the fermentation of paocai and provide effective references for quality control of traditional fermented vegetables.