Sanghuangporous vaninii, as an edible and medicinal macrofungus, represents a high source of polyphenols with considerable antioxidant activities. However, due to the significant differences in polyphenol content and bioactivity caused by different cultivation substrates, its antioxidant mechanism has not been fully determined. In this paper, five groups of S. vaninii fruiting bodies were collected from cultivation substrates from different areas. The ethanol extracts of mulberry sawdust from Haining City (HNMS) had the highest polyphenol content, as well as excellent antioxidant activity. HNMS3, a polyphenol component with promising antioxidant capacity, was further isolated through optimization with different extractants, silica gel column chromatography, and thin layer chromatography analysis. UPLC-Q-TOF-MS analysis showed that HNMS3 was composed of 33 compounds, corresponding to 257 targets of oxidative stress by network pharmacology analysis, which were strongly associated with mental health and neurodegenerative diseases. Protein–protein interaction and molecular docking analysis indicated that eight hub genes (PPARG, IL-6, STAT3, PTGS2, SRC, MTOR, ERS1, and EGFR) are attributed to the regulation of the key compounds hispidin, inoscavin A, inoscavin_C, and phellibaumin B. Consequently, this study obtains S. vaninii polyphenolic component HNMS3 with excellent antioxidant capacity, simultaneously revealing its potential antioxidant mechanisms, providing new insights into the application of S. vaninii.