The relay strip intercropping system of wheat-corn-soybean is widely used in southwest China. However, it is hard to produce soybean stably with this system, since the growth of soybean plants is slower under shading by corn at the seedling stage, and it is compensated by accelerated growth after the symbiotic stage. Soybean plants show excessive vegetative growth due to more rain during the flowering stage, which results in fallen petals, fallen pods and lower yield. This study investigated whether seed treatment with uniconazole powder (0, 2, 4 and 8 mg kg–1 seed) suppresses excessive vegetative growth of soybean plants during the flowering stage and delays senescence of photosynthetically active leaves at the pod-setting stage. If such events are correlated with changes in photosynthesis, they may affect dry matter accumulation and seed yield in the relay stripping system. Uniconazole promoted biomass accumulation from 31 (R3) to 61 (R5) days after flowering (DAF) and seed yield. Seed treatment with uniconazole raised the net photosynthetic rate, stomatal conductance, transpiration rate, and total chlorophyll and chlorophyll a contents. In contrast, uniconazole reduced leaf area index (LAI) from 1 DAF (R1) to 46 DAF (R4) with the increase in uniconazole concentration, whereas, uniconazole significantly increased LAI at 61 DAF, and the greatest promotion occurred at 2 mg kg–1 treatment. The study clearly showed that uniconazole effectively suppressed excessive vegetative growth of soybean during flowering stage, delayed senescence of photosynthetically active leaves at pod-setting stage and induced higher yield, which were related to the changes in photosynthetic rate, chlorophyll content, dry matter accumulation and LAI in the relay strip intercropping system.