To produce a high-quality Kimchi product, molten salt was used for the Kimchi. Changes in the physiochemical properties and functional compounds were analyzed during fermentation. The salinity of bay salt Kimchi was higher than that of the molten salt Kimchi. The fermentation speed of the lactic acid bacteria in the molten salt Kimchi was significantly faster. To evaluate the effects of the salts on the changes in the functional compounds during fermentation, the antioxidant activity, total phenolic compounds (TPC), flavonols, phenolic acids, and glucosinolates in Chinese cabbage were analyzed. In the first 9 days, antioxidants were decreased during this fermentation period and then, increased after that. TPC was slightly increased for all the conditions after 40 days fermentation. Kaempferol was a major flavonol but had a relatively larger decrease in the molten salt Kimchi than in the bay salt samples. Phenolic acid did not show any significant difference among the samples. The glucosinolate contents were significantly decreased in all the conditions of Kimchi during the fermentation period. Consequently, the molten salt greatly affected the fermentation speed of Kimchi and the total characteristics of the Kimchi lactic acid bacteria. Although the functional compounds of Chinese cabbage were decreased during the fermentation of Kimchi, this decrease did not profoundly deteriorate the food quality. Therefore, high-quality Kimchi with enhanced bioactivity will be available if appropriate Chinese cabbages that have enhanced functional compounds are used.