Abstract: The variety of mustard greens is a key factor influencing the formation of fermented pickle quality. By comparing microbial counts, physicochemical indicators, organic acids, glucosinolates and volatile metabolites during the fermentation of mustard (Brassica juncea) varieties, this study assessed differences in fermentation characteristics among distinct mustard cultivars. The results indicated that differences existed in microbial counts, total acidity, and organic acid content during the fermentation of the two mustard (Brassica juncea) varieties. At the end of fermentation, the yeast count in the fermentation broth of Chuanjie No.1 was approximately 1 lg CFU/mL higher than that of Chuanjie No.2. The total acid content of Chuanjie No.2 was 0.156 g/100 g higher than that of Chuanjie No.1, and the increase in lactic acid was 2.3 mg/mL higher. In terms of glucosinolates and their primary volatile metabolites, the total glucosinolate content in fresh Chuanjie No.2 was 50.09% higher than that in Chuanjie No.1, Allyl isothiocyanate, 3-butenyl isothiocyanate, phenethyl isothiocyanate, 3-butenonitrile, and acetonitrile were key differential glucosinolate metabolites that distinguished the flavor profiles of Chuanjie No.1 and Chuanjie No.2 during different fermentation stages. Correlation analysis indicated that total glucosinolates showed a negative correlation with bacteria and lactic acid bacteria during fermentation. Volatile glucosinolate metabolites of the isothiocyanate class showed a negative correlation with bacteria and lactic acid bacteria, while exhibiting a positive correlation with total glucosinolate content. The glucosinolate content in different mustard varieties might influence the growth and metabolism of fermenting microorganisms as well as fermentation quality, leading to significant variations in the final product's flavor. The experimental results provided a theoretical basis for the targeted selection of high-quality fermented mustard.