Ginkgo biloba seed (GBS) contains rich nutrients, such as starch, protein, oil, and trace components, such as flavonoids and terpene lactones. Due to its high protein content, it can be used as a raw material for fermentation and brewing. In this study, GBS was selected as the object of a fermentation process optimization test. Six kinds of fermentation starter were selected to brew ginkgo wine. The results showed that different fermentation starters have significant impacts on the composition of the wine. The yeast group had higher total sugar content and comprehensive evaluation scores than the Jiuqu group, while the total acid and total free amino acid contents showed the opposite result. The total flavonoid and total terpene lactone contents of the yeast group were 21.0% and 12.8% higher than those of the Jiuqu group, respectively. However, the 4′-O-methylpyridoxine (MPN) and 4′-O-methylpyridoxine-5′-glucoside (MPNG) contents of the yeast group were also 12.6% and 2.3% higher than those of the Jiuqu group, respectively. The common volatile components in the two groups of samples were isoamyl alcohol, phenethyl alcohol, ethyl octanoate, and phenethyl acetate. The antioxidant capacity of ginkgo wine fermented by yeast was significantly higher than that of the Jiuqu group sample.