ABSTRACT Isoflavonoids, which are abundant in soybeans, increase the utility value of soybean products and mediate plant defenses against diverse stresses. In this study, integrated transcriptomic and ultra‐performance liquid chromatography (UPLC) analyses revealed that Phytophthora sojae ( P. sojae ) infection remodels the isoflavonoid biosynthesis pathway. Exogenous isoflavonoid application significantly increased soybean resistance to P. sojae , suppressing lesion expansion by more than 70% and inhibiting both reactive oxygen species accumulation and host cell death. Resistant evaluation of 228 soybean germplasms revealed 48 germplasms resistant to P. sojae isolate JS08‐12, 42 germplasms resistant to isolate W210, and 38 elite germplasms exhibiting resistance against both W210 and JS08‐12. Compared with that of the susceptible germplasm (1850.24 μg g −1 ), the resistant soybean germplasm presented 35.35% higher total isoflavonoids (2504.29 μg g −1 ), with significant increases in six compounds: 6″‐O‐malonylgenistin (+33.04%), 6″‐O‐malonyldaidzin (+43.35%), genistin (+43.34%), daidzin (+43.97%), genistein (+5.99%), and 6″‐O‐acetylgenistin (+5.48%). Importantly, the elite germplasm YZS180, YZS210, YZS073, and YZS052 presented significantly high levels of seed isoflavonoids (> 3500.00 μg g −1 ) and strong resistance. We further investigated the crosstalk between abscisic acid (ABA) and isoflavonoids. This study identifies isoflavonoids as defense metabolites against P. sojae and provides elite genetic resources for breeding soybeans with integrated disease resistance and nutritional quality.