In response to shading, plant leaves acclimate through a range of morphological, physiological and biochemical changes. Plants produce a myriad of structurally and functionally diverse metabolites that play many important roles in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. To develop a clearer understanding of the effects of shade on soybeans at different growth stages, a comprehensive, three-year, stage-wise study was conducted. Leaf area, leaf thickness, stem diameter, chlorophyll contents, photosynthetic characteristics and other morphological and physiological features were measured along with biochemical assays for antioxidants such as superoxide dismutase, peroxidase and caralase and yield attributes of different soybean genotypes (Guixia 2, Nandou12, Nandong Kang-22, E61 and C103) under shading nets with 50% light transmittance. It was observed that early shading (VER1 and VER2) significantly decreased main stem length and main stem length/stem diameter. Later shading (R1R8 and R2R8) had significant effects on morphological characters such as branch number and pod height. In Nandou 12, the protein contents in plants shaded at R1R8, R2R8 and R5R8 were 9.20, 8.98 and 6.23% higher than in plants grown under normal light levels (CK), respectively, and the crude fat content was 9.31, 10.74 and 4.28% lower. The influence of shading in the later period on anatomy was greater than that in the earlier period. Shading reduced the light saturation point (LSP), the light compensation point (LCP) and the maximum photosynthetic rate (Pnmax), and increased the apparent quantum yield (AQ). Shading also increased the antioxidant enzyme activity in the plants, and this increase was greater with early shading than late. The variability in the chlorophyll (a + b) content and the chlorophyll a/b ratio in R2 stage plants was less than in R5 stage (VER5) plants. Similarly, the activity of antioxidant enzymes in R2 after returning the plants to normal light levels (VER2) was lower than in R5 after relighting (VER5). Compared with later shading, the early shading had a greater effect on the photosynthetic and related characteristics. The longer the shading time, the greater the adverse effects and the less able the plants' were to recover. The data collected in this study contribute to an understanding of the physiological mechanisms underlying the early and late growth stage acclimation strategies in different soybean genotypes subjected to shade stress.