Soybean in relay intercropping is initially exposed to a shade environment, followed by exposure to full sunlight after the harvesting of primary crops, e.g., maize. Therefore, soybean’s ability to acclimate to this changing light environment determines its growth and yield formation. However, the changes in soybean photosynthesis under such light alternations in relay intercropping are poorly understood. This study compared the photosynthetic acclimation of two soybean varieties with contrasting shade tolerance, i.e.,Gongxuan1(shade-tolerant) andC103(shade-intolerant). The two soybean genotypes were grown in a greenhouse under full sunlight (HL) and 40% full sunlight (LL) conditions. Subsequently, after the fifth compound leaf expanded, half of the LL plants were transferred to a high-sunlight environment (LL-HL). Morphological traits were measured at 0 and 10 days, while chlorophyll content, gas exchange characteristics and chlorophyll fluorescence were assayed at 0, 2, 4, 7 and 10 days after transfer to an HL environment (LL-HL). Shade-intolerantC103showed photoinhibition 10 days after transfer, and the net photosynthetic rate (Pn) did not completely recover to that under a high light level. On the day of transfer, the shade-intolerant variety,C103, exhibited a decrease in net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (E) in the low-light (LL) and low-light-to-high-light (LL-HL) treatments. Additionally, intercellular CO2concentration (Ci) increased in low light, suggesting that non-stomatal factors were the primary limitations to photosynthesis inC103following the transfer. In contrast, the shade-tolerant variety,Gongxuan1, displayed a greater increase inPn7 days after transfer, with no difference observed between the HL and LL-HL treatments. Ten days after transfer, the shade-tolerantGongxuan1exhibited 24.1%, 10.9% and 20.9% higher biomass, leaf area and stem diameter than the intolerantC103. These findings suggest thatGongxuan1possesses a higher capacity to adapt to variations in light conditions, making it a potential candidate for variety selection in intercropping systems.