Nitrogen (N) is an essential component of photosynthetic apparatus. However, the mechanism that photosynthetic capacity is suppressed by N is not completely understood. Photosynthetic capacity and photosynthesis-related genes were comparatively analyzed in a shade-tolerant species Panax notoginseng grown under the levels of low N (LN), moderate N (MN) and high N (HN). Photosynthetic assimilation was significantly suppressed in the LN- and HN-grown plants. Compared with the MN-grown plants, the HN-grown plants showed thicker anatomic structure and larger chloroplast accompanied with decreased ratio of mesophyll conductance (gm ) to Rubisco content (gm /Rubisco) and lower Rubisco activity. Meanwhile, LN-grown plants displayed smaller chloroplast and accordingly lower internal conductance (gi ). LN- and HN-grown individuals allocated less N to light-harvesting system (NL ) and carboxylation system (NC ), respectively. N surplus negatively affected the expression of genes in Car biosynthesis ( GGPS , DXR , PSY , IPI and DXS ) and non-net carboxylative process (CEF-PSI). The LN individuals outperformed others with respect to non-photochemical quenching. The expression of genes ( FBA, PGK, RAF2, GAPC, CAB, PsbA and PsbH ) encoding enzymes of Calvin cycle and structural protein of light reaction were obviously repressed in the LN individuals, accompanying with a reduction in Rubisco content and activity. Correspondingly, the expression of genes encoding RAF2 , RPI4 , CAB and PetE were repressed in the HN-grown plants. LN-induced depression of photosynthetic capacity might be caused by the deceleration on Calvin cycle and light reaction of photosynthesis, and HN-induced depression of ones might derive from an increase in the form of inactivated Rubisco and the deprivation of photoprotection.