Polyphenols are major functional components of the medicinal mushroom Inonotus obliquus. Compared with the wide application of surfactants in medicinal mushroom polysaccharide production, using surfactants to enhance mushroom polyphenol production and antioxidant activity is a relatively new approach. For the first time, in the present study, we evaluated the effect of Tween-20 on the growth-associated generation of different compositions and antioxidant activity expression of exo-polyphenol product (EPC) and endo-polyphenol product (IPC) of liquid cultured I. obliquus. The IC50 values against 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals of EA-EPC, NB-EPC, and IPC from the Tween-20 (5.0g/l on Day 1) adding medium were between 40 and 47mg/l, significantly (p < 0.05) lower than the control group (96–112mg/l). Phenolic acids, i.e., ferulic acid and gallic acid, and flavonoids, i.e., epicatechin-3-gallate (ECG), epigallocatechin-3-gallate (EGCG), and naringin, were the main components in EPC and IPC analyzed by HPLC. The production of ferulic acid, ECG, EGCG, and naringin was significantly increased by 106.0%, 157.7%, 37.3%, 75.2% in EA-EPC, 372.9%, 133.7%, 117.3%, 19.4% in NB-EPC, and 10.4%, 102.7%, 57.7%, 322.2% in IPC. The antioxidant activity expression of EA-EPC, NB-EPC, and IPC from both the control and Tween-20 media was highly correlated with the growth-associated generation of these flavonoids during fermentation. The significantly higher antioxidant activity of EPC and IPC from the Tween-20 medium compared with the control was also attributed to the higher content of the flavonoids. The strategy of supplementation of surfactants has the potential for other medicinal mushroom fermentation processes to enhance the production of highly bioactive flavonoids.