The phenolic compounds (PC) of soybeans (Glycine max (L.) Merrill) varies mainly based on factors like genetics, the environment, and also the food processing techniques used. The effect of storage time and temperature on the phenolic acids and isoflavones composition of raw soybean flour (RWSF) and roasted soybean flour (RSF) were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the analysis results, 56 PC and free amino acids were detected in the RWSF and RSF. The total phenolic content (TPC) was 301.59 µg/g in the control RWSF and 257.47 µg/g in the control RSF. In the analysis, eight types of phenolic acids and one flavonoid group belonging to the isoflavone group were detected. When comparing storage conditions of RWSF, 24 and 48 weeks of storage showed higher concentration of phenolic acids. In RSF, the percentage of total acetyl glucosides was high, but the outcome was reversed after 2 weeks. This study had identified that the composition of PC in RWSF and RSF were affected when the storage temperature increased and the storage time lengthened.