Effects of shading on photosynthesis characteristics and leaf anatomical structure of Emmenopterys henryi seedlings were studied using four shading treatments including full sunlight (L0), 60% sunlight (L1), 25% sunlight (L2), and 15% sunlight (L3), respectively. The results showed that:(1) Shading had an significant effect on the net photosynthetic rate (P_n), transpiration rate (T_r), stomatal conductance (G_s), stomatal limitation value (L_s), intercellular CO₂ concentration (C_i), and vapor pressure deficit (V_pdl) of E. henryi seedlings. The diurnal changes of P_n and T_r under L0 and L1 treatments showed obviously bimodal curves, and the "noon break" appeared at 12:00. Their changes under L2 and L3 treatments were relatively mild, and the "noon break" were not obvious. The variation of G_s was basically consistent with that of P_n. The variation of C_i showed a tendency of declining slowly at early stage and rising rapidly later. Compared with the control, the shading promoted significantly increase of the C_i. Both L_s and V_pdl showed the arc changes of slow rising in advance and decreasing in the latter stage, and the daily averages under shading were lower significantly than the control. The order of daily averages of P_n and T_r was L1 > L0 > L2 > L3. (2) The photosynthesis-light response characteristics of E. henryi seedlings under four light regimes were obviously different. The seedlings grown under the full sunlight condition could maintain a higher P_n without obvious photoinhibition, showing a certain degree of shading-tolerance and light-demanding. The maximum net photosynthetic rate (P_max), dark respiration rate (R_d), and apparent quantum efficiency (AQY) under L1 treatment increased more significantly than the control. Therefore, the E. henryi seedlings had some plasticity to light intensity. The mild shading was beneficial to the improvement of photosynthetic efficiency. Serious shading (L2 and L3) resulted in a significant decrease of light compensation point (LCP) and light saturation point (LSP), which was beneficial to make full use of weak light. But they resulted in P_max and R_d decrease obvious, which inhibited photosynthetic efficiency. (3) The shading significantly affected the stomatal distribution on leaves surface of E. henryi seedlings. Under shading condition, the stomata density decreased significantly, and the stomata length, the stomata width, and single stomatal area was similar. (4) Under shading, the leaf thickness decreased, the upper epidermis thickened, and the lower epidermis thinned. The thickness of palisade tissue (PT) decreased and sponge tissue (ST) was not fully developed, and the value of PT/ST increased. Moreover, the number of vessel in vascular bundle and the vessel diameter increased significantly, which promoted the transport of water in leaves. (5) In order to meet the needs of growth and development of E. henryi seedlings in cultivation, we suggested that the effective radiation intensity should be above 60% of natural light intensity.