In intercropping systems, high-positioned crops often exert shading stress on low-positioned crops, thus affecting the agronomic characteristics of the low-positioned crops. This study determined the mechanisms of photosynthetic, physiological and yield variations among peanut cultivars under shading stress. Four peanut cultivars, S60, C4, P12, and YS151, were grown in the field and subjected to shading stress for 77 days during reproductive stages. S60 and P12 showed lower yield and reduced biomass accumulation than C4 and YS151 under shading stress. Shading stress induced higher antioxidant enzyme activities in S60 and P12, relative to C4 and YS151. Under shading stress, S60 and P12 showed a higher light-trapping capability than C4 and YS151, which was associated with changes in chlorophyll (Chl) a and b contents, and Chl a/b ratio. The net photosynthetic rate, stomatal conductance and transpiration rates of C4 and YS151 were decreased, but the intercellular CO2 concentration increased under shading stress. The results demonstrated that non-stomatal limiting factors decreased the photosynthetic capacity of peanut under shading stress. The maximum photochemical efficiency of PSⅡ(Fv/Fm) and non-photochemical quenching (NPQ) were higher in S60 and P12 than in C4 and YS151 under shading stress. These results suggest that S60 and P12 could absorb more light energy from weak light environments for photosynthesis than C4 and YS151 and dissipate the excess energy in the form of heat to improve their light protection ability. This study explains the inter-variety differences in shading stress tolerance in peanut and provides physiological parameters for guiding the selection of shade-tolerant cultivars.