Intercropping maize and soybean affects soybean yield by reducing photosynthesis and pod setting. In a study comparing four soybean cultivars, ZH39 and QH34 had higher yields than HD19 and HD20 in intercropping systems. The number of pods, seeds, and harvest index were lower in intercropping, but ZH39 and QH34 had better yield components than HD19 and HD20. Leaf photosynthetic parameters changed with intercropping, but not significantly among cultivars. The crop growth rate between flowering and seed development was lower in intercropped soybean, but not different between cultivars. The amount of reproductive biomass at seed development stage influenced yield differences among cultivars. High-yielding cultivars in intercropping had more reproductive structures at seed development, leading to higher yields.