Asynchronous seed development complicates soybean response to post-flowering high-temperature (HT) stress. To elucidate the mechanisms underlying HT-induced yield reduction after flowering, soybean plants were subjected to a six-day HT treatment in a greenhouse beginning at the opening of the first flower. HT reduced seed number and impaired pod and seed development at the initial flowering nodes, as evidenced by the decline in size and fresh weight. HT downregulated genes related to DNA replication, cell division, lipid metabolism, and secondary metabolism. Notably, auxin signaling and cell cycle factors emerged as central regulatory networks governing seed development. HT downregulated the expression of critical cell cycle components, including cyclins, kinesins, MAD2, and RAD, the latter two containing auxin-responsive elements. Moreover, HT reduced auxin levels in fertilized ovaries, while exogenous auxin (0.1 nM 1-Naphthaleneacetic acid) treatment alleviated HT-induced seed developmental restriction, mainly by increasing cell number and size. Auxin treatment further improved pod set, pod and seed number, and grain weight under HT stress. These results suggest that the cell cycle suppression is determinant for growth retardation in synergy with reduced auxin levels in soybean seeds, and auxin supplementation could enhance soybean adaptation to post-flowering HT stress.