【Objective】 The annual variations and the correlation between the photosynthetic properties and flavonoids content in the leaves of female, male and golden-leaf (varieties of bud mutation) Ginkgo biloba were investigated to provide a references for the selection and breeding of robust G. biloba species, promotion of new varieties, and cultivation seedlings for harvesting leaves. 【Method】 Changes in photosynthetic pigments, chlorophyll fluorescence parameters, and flavonoid composition and content from April to November were studied in the leaves of female, male and grafted golden-leaf G. biloba trees. 【Result】 During the entire year, the water content in male trees was lower than that in female and golden-leaf trees in three G. biloba species, especially during the high-temperature summer period from June to September. Although the water content, relative leaf area and chlorophyll content in the male and golden-leaf G. biloba trees were lower than those in female trees, especially from May to August, their relative leaf area increased faster than the female trees. Furthermore, although the photochemical quenching (qP) and non-photochemical quenching (NPQ) coefficients were higher in the female trees than those in the male or golden-leaf tree, the maximum photochemical efficiency (F_v'/F_m') was lower in the female trees than that in the male and gold leaf tree. The annual variations in three flavonoid glycosides such as quercetin and total flavonoid contents in three G. biloba species revealed two high points, one in April to May and another in September. The highest level of the total flavonoid content in leaves was observed in September, and the total flavonoid content in the three tree species was in the following order: golden-leaf > male > female. The chlorophyll, carotene and quercetin contents in male trees were positively correlated with each other; however, a significant positive correlation between chlorophyll a, carotene, and total flavonoids was found in the female trees. The golden-leaf tree leaves maintained a golden yellow color from April to June owing to the lower chlorophyll content than their male and female counterparts during this period. However, their leaves changed from yellow to green after July, and their photosynthetic, flavonoid changes were closer to those of the male trees. Furthermore, the flavonoid content in golden-leaf trees was higher than that in the male and female trees. 【Conclusion】 The best harvesting stage for ginkgo leaves was in September in the Nanjing region of China; male and golden-leaf trees exhibited greater conduciveness to the cultivation of leaf-using forest; and the female trees exhibited higher stress resistance than male and golden-leaf trees. Golden-leaf G. biloba tree has an ornamental value and excellent economic characteristics, which makes it worth developing and utilizing vigorously in the future.