The nutrition bag cultivation was used to investigate the effect of fertilization on growth and photosynthetic physiology of machilus（Phoebe zhennan）polyembryonic seedlings. In the study, three types of seedlings i.e. single embryo seedlings(D), bigger one of twin embryo seedlings (SD), and smaller one of twin embryo seedlings (SX) were selected and planted as experimental material. The age of seedlings for planting was 45 d and the rhizome was preliminary lignification. The experiment was set as three levels of fertilizer application, i.e. control (CK, 0 g per bag), medium level (M, 0.2 g per bag) and high level (H, 0.3 g per bag). Compound fertilizer was applied and the amount of fertilizer was divided into 4 parts and began to apply in early July and ended in early September with the interval of 20 d. The determination of seedling growth and physiological indexes of photosynthesis were conducted in mid of August and mid of October. The results showed that： (1) The medium level(M) of fertilization significantly promoted the height and ground diameter growth of three types seedlings, while high level(H) of fertilization showed the effect of promoting first and then inhibition, and indicated the excessive fertilization. (2) The medium level(M) of fertilization significantly promoted the synthesis of chlorophyll of three types of seedlings, prolonged the functional period of leaves, increased net photosynthetic rate and stomatal conductance, and furthermore improve the ability of photosynthesis of the seedlings under high light intensity and the environment of high CO₂ concentration. (3) The fertilization can decrease the light compensation point (LCP) and CO₂ compensation point (CCP) of seedlings, and increase the light saturation point (LSP) and CO₂ saturation point (CSP), promoting seedlings to adapt to the environment and accumulate more organic matter. Whereas the high amount of fertilization on the photosynthetic indicators of seedlings also showed the role of promotion first and then inhibition. The results showed that synthesis of photosynthetic pigment in all machilus seedlings and photosynthetic efficiency as well as environmental adaptability are enhanced under moderate fertilizer application, which helped to promote the growth of seedlings; the medium level (M) of fertilizer application can rapidly reduce the gap between the growth indicators of bigger one of twin embryo seedlings and single embryo seedlings . and also plays a promoting role on the growth of smaller one of twin embryo seedlings. The results indicated the important significance for the conservation of machilus germplasm resources, and for the promotion of qualified rate of seedlings and reduction of the cost of raising seedling.