Abstract: An experiment of combining application of Mg, Zn and Mo fertilizers under the foliage spraying with different levels was arranged to study effects of the fertilization on leaf biomass, main medicinal constituent contents and their yields per plant of ginkgo seedlings on the basis of an orthogonal design in greenhouse. The results show that the different combinations of Mg, Zn and Mo fertilizers have significant effects on leaf biomass, total flavonoid content and its yield per plant, terpene trilactone content and its yield per plant of ginkgo seedling. The treatments of Mg4Zn3Mo2, Mg1Zn4Mo2, Mg2Zn4Mo3, Mg4Zn4Mo2 and Mg4Zn4Mo2 are suitable to enhance leaf biomass，total flavonoid content and its yield per plant, terpene trilactone content and its yield per plant, respectively. The primary relations of Mg, Zn and Mo effect on leaf biomass，total flavonoid content and its yield per plant are MgMo Zn. The primary relations of Mg, Zn and Mo effect on terpene trilactone content and its yield per plant are Zn MoMg, and MgZnMo respectively. Spraying Mg, Zn and Mo fertilizers could correspondingly promote total magnesium, total zinc, total molybdenum contents, while praying Zn and Mo fertilizers have little influences on total magnesium contents. Spraying Mg fertilizer could promote total zinc contents under high levels of Mg, while praying Mo fertilizer could promote total zinc contents under low levels of Mo. Spraying Mg and Zn fertilizers have little influences on total molybdenum contents. The Mg fertilizer has bad effect on total flavonoid content and has good effect on terpene trilactone content and its yield per plant. The high level of the Zn fertilizer could promote total flavonoid and terpene trilactone contents, but the low level of Zn has small or bad effects on them. The low and moderate levels of the Mo fertilizer could promote total flavonoid and terpene trilactone contents, but the high level of Mo has small or bad effects on them.