The aim of this study was to investigate the effects of different starter cultures on fermented mustard quality. Brassica juncea was used as the raw material; three inoculated fermentation groups were established, namely LPMA (comprising Lactiplantibacillus plantarum, Enterococcus faecium, and Lactobacillus pentosus), LPA (L. plantarum and L. pentosus), and LP (L. plantarum alone), with a natural fermentation group (NF) serving as the control. Overall, the LPMA group achieved the highest sensory score (82.86). A total of 257 non-volatile metabolites were identified by liquid chromatography–tandem mass spectrometry (LC-MS/MS) across the three experimental and one control groups, encompassing 11 major classes that included organic acids, flavonoids, and vitamins. Principal component analysis revealed a clear metabolic distinction between the inoculated groups (LPMA, LPA, LP) and the NF group, with 67 key differential metabolites being identified. Organic acids (e.g., succinic acid), umami amino acids (L-glutamic acid), esters (e.g., phenylacetic acid ethyl ester), and bioactive compounds (e.g., chlorogenic acid) were significantly enriched in the inoculated groups. Conversely, the NF group exhibited elevated levels of bitter compounds (4-oxoproline), biogenic amines (phenylethylamine), and potentially harmful substances (phytanic acid). Among the inoculated groups, LPMA demonstrated the most favorable metabolic profile, with significantly elevated levels of daidzein, hesperetin, β-carotene, and vitamin B2, while effectively suppressing phytanic acid accumulation. These findings confirm that compound starter cultures can enhance the flavor, functional activity, and food safety of fermented mustard and provide theoretical support for the development of fermentation agents with improved stability and flavor harmony.