An experiment was set up to investigate physiological responses of soybeans to silicon (Si) under normal light and shade conditions. Two soybean varieties, Nandou 12 (shade resistant), and Nan 032–4 (shade susceptible), were tested. Our results revealed that under shading, the net assimilation rate and the plant growth were significantly reduced. However, foliar application of Si under normal light and shading significantly improved the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and decreased intercellular carbon dioxide concentration (Ci). The net photosynthetic rate of Nandou 12 under normal light and shading increased by 46.4% and 33.3% respectively with Si treatment (200 mg/kg) compared to controls. Si application also enhanced chlorophyll content, soluble sugars, fresh weight, root length, root surface area, root volume, root-shoot ratio, and root dry weight under both conditions. Si application significantly increased the accumulation of some carbohydrates such as soluble sugar and sucrose in stems and leaves ensuring better stem strength under both conditions. Si application significantly increased the yield by increasing the number of effective pods per plant, the number of beans per plant and the weight of beans per plant. After Si treatment, the yield increased 24.5% under mono-cropping, and 17.41% under intercropping. Thus, Si is very effective in alleviating the stress effects of shading in intercropped soybeans by increasing the photosynthetic efficiency and lodging resistance.