In vitro grown cabbage (Brassica oleracea var. capitata) seedlings exposed to excess molybdenum (Mo) ions exhibited severely reduced plant growth at the cotyledonary stage. Adding 80 mM proline (Pro) to the Mo-treated medium could help 50% seedlings to overcome the toxicity and grow true leaves. Under excess Mo stress, seedlings accumulated blue/purple anthocyanin in their cotyledons and hypocotyls. The anthocyanin content under Mo with 40 mM Pro was 4-fold higher than the control medium, MS with 40 mM Pro. The presence of Pro in the excess-Mo condition reduced chlorophyll a, whereas the chlorophyll b content was much higher than the control media of MS with and without Pro. Moreover, supplementing various concentrations of Pro into the Mo-stressed condition promoted the seedlings with higher antioxidant enzyme activities of superoxide dismutase, ascorbate peroxidate, and catalase. In addition, genes in the anthocyanin biosynthesis and accumulation pathways, phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), flavonone 3-hydroxylase (F3H), leucoanthocyanidin dioxygenase (LDOX), and glutathione-S-transferase (GST), were all upregulated. Our study indicated that, under excess Mo stress, the antioxidant activity of cabbage seedlings was induced in an attempt to protect plants from the Mo-induced toxicity and exacerbated growth. Pro, on the other hand, functioned in producing higher antioxidant enzyme activity to partially help recover plant growth.