Soybean is a widely cultivated crop, however, its growth and development is very sensitive to light. Shade-tolerance of cultivar is very important in intercropping. The objective of this study was to understand light acclimation of different soybean cultivars grown under different shade treatments and why the photosynthetic capacity of soybean decreased in shade. The chlorophyll content (Chl a, Chl b, and Chl a+b), apparent quantum efficiency (AQE), the value of electrons produced per photon (α), maximal quantum yield of primary photochemistry (φ Po), quantum yield for electron transport (φ Eo), efficiency/probability that an electron moves further than QA − (ψ Eo), and performance index on the absorption basis (PIABS) of shade treatment increased significantly, while efficiency/probability with which an electron from the intersystem electron carriers is transferred to reduce end electron acceptors at the PSI acceptor side (δ Ro), quantum yield for reduction in end electron acceptors at the PSI acceptor side (φ Ro), total PI, measuring the performance up to the PSI end electron acceptors (PItotal) dropped significantly. The chlorophyll content, AQE, α, φ Po, φ Eo, ψ Eo and PIABS of cultivar L32 were higher than those of L29. These results showed that shade increased the light-intercepting and utilization ratio to low light and the activity of PSII of soybean plants, but the energy transport from PSII to PSI was blocked, which was the reason why the photosynthetic capacity was inhibited. Shade-tolerant cultivar L32 had higher PSII activity and energy transport from PSII to PSI than L29 in shade, so shade-tolerant cultivar exhibited higher photosynthetic capacity and yield than shade-sensitive in shade.