Maize-soybean relay intercropping pattern, with highly economic, ecological and environmental significance, is widely applied in southwestern China. However, growth of soybean seedlings may be depressed by maize shade in this cropping pattern. The objective of this paper was to study the photosynthetic responses of soybean seedlings to maize shading in relay intercropping system in terms of morphological plasticity and photosynthetic parameters compared with mono-cropping system. A field experiment was conducted to compare gas exchange, chlorophyll fluorescence parameters, pigments contents, leaf carbon and nitrogen contents, leaf area index and dry matter accumulation of two soybean cultivars in two cropping patterns, i.e., soybean mono-cropping and maize-soybean relay intercropping. Compared with the mono-cropped seedlings, soybean seedlings intercropped with maize had significantly lower net photosynthetic rate (P_n)(-37.9%), transpiration rate (T_r) (-42.4%) and stomatal conductance (G_s) (-54.2%) due to low available light, but there was non-significant difference in two soybean varieties. The intercellular carbon dioxide concentration (C_i) and F_v/F_m were not changed significantly, in comparison with the seedlings under mono-cropping. Additionally, reductions in photosynthetic rate induced by maize shading was correlated significantly with stomatal conductance. The maize shading-induced depressions of photosynthetic rate may be attributed to stomatal limitation and energy deficiency in CO₂ assimilation process. Leaf carbon contents, leaf weight, leaf area index, root dry weight, total biomass and root/shoot ratio was also reduced because of maize shading, and significant difference was found between the two soybean varieties, which indicated that Nangdou12 might be a better cultivar to be relay intercropped with maize in Southwest China. The correlation analysis indicated that the relative reduction in biomass was caused by the decline in leaf area index rather than P_n. Although automatic regulation of light-harvesting efficiency in terms of total nitrogen contents, total chlorophyll contents and chlorophyll b contents was significantly improved in soybean seedlings in relay intercropping condition, it could not compensate the decline of light interception caused by the reduced light interception area. Therefore, the growth parameters may be more important index for assessing the adaptation of soybean cultivars to low light condition in intercropping system than ecophysiological parameters merely at unit leaf level.