The impact of increased shading stress on agronomic traits, photosynthetic performance and antioxidants activities in leaves of two soybeans cultivars (D16 and E93) was studied. Soybean seedlings were grown in pots and exposed to no shade (S0), slight shade (S1), moderate shade (S2), and heavy shade (S3). Our findings showed that under the S3 in both cultivars, leaf fresh weight (LFW), specific leaf area (SLA) and leaf thickness decreased significantly, accompanied by a reduction in photochemical parameters including the maximum quantum yield (Fv/Fm) and electron transport rate (ETR). Furthermore, compared to S0, S1 significantly increased the ETR, sucrose content and the activity of catalase (CAT) in both D16 and E93 cultivars while S2 and S3 decreased the activity. However, under all treatments of shading stress, the antioxidant activities of superoxide dismutase (SOD) and peroxidase (POD) were lowered in both cultivars. Such morphological and physiological plasticity to adapt S1 compensates for the decrease in biomass and leads to seed weight compared to that obtained with an amount of normal light. Through configuring the space in the intercropping systems, S1 could be helpful for optimum growth and yield. Redesigning photosynthesis through S1 for the intercropping systems could be a smart approach.