We analyzed the seed production of soybean (Glycine max (L.) Merr.) plants growth of cultivars ‘Fukuyutaka,’ popular in western Japan, and ‘Misato-zairai,’ local to Mie Prefecture, grown under shade from beginning bloom (R1) stage. To simplify the sink–source relationship, all branches and buds were removed during the shading. In both cultivars, shading decreased pod and seed numbers and seed weight. These were correlated linearly with pod growth rate after flowering, except that the relationship with seed weight was quadratic. Shading also decreased total dry weight, but had little effect on leaf area index (LAI) or SPAD at the beginning seed stage (R5). Pod growth rate after flowering was correlated with crop growth rate (CGR) during pod set. CGR was corelated with net assimilation rate (NAR), but not average LAI during pod set. Stem weight at maturity was corelated with LAI at R5. ‘Misato-zairai’ responded to shading similarly to ‘Fukuyutaka,’ but with large increases in CGR with NAR and in stem weight with LAI at R5.