The massive leaf shedding in monoculture soybeans post-anthesis detrimentally impacts production, whereas relay strip intercropping can extend leaf area duration to enhance overall productivity. To reveal the reasons for leaf shedding in monoculture soybeans and how it affects the physiological and biochemical functions of source and sink organs, we conducted a four-year field experiment and a leaf-removal simulation experiment in relay strip intercropped soybeans to measure the phenotypic and physiological traits of leaves and nodules. The results showed that the strong self-shading of leaves in monoculture soybeans led to extensive defoliation, while the superior light environment in relay strip intercropped soybeans can promote the maintenance of a higher leaf area, nodule growth, and photosynthetic carbon allocation. With increasing leaf removal, leaf growth increased first and then decreased, and leaf defoliation gradually decreased. Extensive leaf-removal reduced Rubisco activity and sucrose phosphate synthase (SPS) activity in leaves, as well as the content of sucrose, malate, ATP, and energy charge (EC) in nodules, with a trade-off between leaf mass enhancement and weakened nodule growth. Notably, moderate leaf-removal could balance compensation and consumption. The total non-structural carbohydrates (TNC) in roots, N and Ureide in leaves and pods increased in unison, achieving the synergies between leaves and nodules to maintain a higher energy status and growth rate. Our study highlights that the favorable light environment in relay strip intercropping system shapes the coordinated functioning of above-ground and below-ground source-sink organs and effectively promoting photosynthesis and nitrogen fixation. These findings contribute to a better understanding of the underlying mechanisms of effective resource utilization in different cropping patterns, aiding in the sustainable development of food production.