Shading conditions adversely affect flower-number and pod-number of soybeans under maize-soybean relay-intercropping (MSR). Here we reveal that leaf-removal from maize-canopy improves the photosynthetically active radiation (PAR) transmittance and dry-matter production (DMP) of soybean (especially during the co-growth phase), and compensates the maize seed-yield loss by considerably increasing soybean seed-yield. In a two-year experiment with MSR, maize-plants were subjected to different leaf-removal treatments to increase the PAR-transmittance of soybean; removal of the topmost two-leaves (R2), four-leaves (R4), six-leaves (R6), with no-removal of leaves (R0). Leaf-removal treatments improved the PAR-transmittance, photosynthetic-rate, and morphological-characteristics of soybean under MSR. At 90 days after sowing, the dry-matter of pods, and seeds was increased by 25%, and 32%, respectively under R6 than R0. Importantly, enhanced PAR-transmittance and DMP under R6 enabled soybean to initiate a greater number of flowers 182.2 plant-1 compared to 142.7 plant-1 under R0, and it also decreased the flower-abscission (by 13%, from 54.9% under R0 to 47.6% under R6). These positive responses increased the pod-number by 49% and seed-number by 28% under R6 than R0. Overall, under R6, relay-intercropped soybean produced 78% of sole-soybean seed-yield, and relay-intercropped maize produced 81% of sole-maize seed-yield and achieved the land equivalent ratio of 1.59.