Elevated CO2 increases seed production more in plant species that form a symbiotic association with N2-fixing bacteria than in species without such association. We studied the mechanism of the increase of seed production with elevated CO2 using nodulated soybean (Glycine max cv. Enrei) and its non-nodulated isogenic line (cv. En1282). Increase in seed production with elevated CO2 was observed in nodulated Enrei but was not in non-nodulated En1282. The increase in seed production in Enrei was explained by the increase in the rate of dry mass production during the reproductive period. This increase was associated with the increase in N assimilation in the reproductive period and the seed N concentration that remained the same as that at ambient CO2. Dry mass production and nitrogen assimilation did not increase in the vegetative phase in both lines. These results accorded with the amount of nodules in Enrei that increased at elevated CO2 especially after flowering. We conclude that the increase in N assimilation in the reproductive period would be the key for increasing soybean yield in the future high-CO2 world.