A methanolic extract from a soybean broth fermented by Paecilomyces militaris was analysed by HPLC–PDA–HRMS. It mainly contained mannitol, uracil, adenosine, cordycepin, daizein, genistein, and three new isoflavone glycosides. The isoflavonoids were isolated by preparative HPLC and identified with the aid of HPLC–PDA–HRMS, 1H NMR, 13C, H–H COSY, HMBC, and HMQC NMR analysis as: 7,4′-dihydroxyisoflavone-7-O-(4′′-O-methyl)-β-d-glucopyranoside, 7,4′-dihydroxy-6-methoxyisoflavone-7-O-(4′′-O-methyl)-β-d-glucopyranoside, and 5,7,4′-trihydroxyisoflavone-7-O-(4′′-O-methyl)-β-d-glucopyranoside. The three novel compounds are transformation products of soybean isoflavones. The results of metabolites analysis revealed that the fermentation broth reserved the main functional molecules of soybean and P. militaris or Cordyceps militaris. This suggested that soybean fermented with P. militaris may be able to create a combined healthy food. However, isoflavones are also parts of anti-nutrients of soybean products, and cordycepin is a known antibiotic. This means that the fermentation broth may not suit to be used as normal food. At the same time the safety and bioactivity of the novel methylated glycosides need also further approval.