Phellinus igniarius is a very important, high-value medicinal fungus; flavonoids are one of its most important components. Methods to improve the content of flavonoids in Ph. igniarius deserve attention. Moreover, because of the low production of Ph. igniarius, it is also important to increase biomass. This study demonstrated that exogenous salicylic acid (SA) treatment can significantly promote the accumulation of total flavonoids and biomass in Ph. igniarius. After treatment with different concentrations of SA, the flavonoid content and biomass of Ph. igniarius increased by 20.54-93.15% and 31.90-43.92%, respectively, compared with the control, with flavonoid content and biomass reaching maximum values of 300 μM and 200 μM SA, respectively. Additionally, we found that SA induced the biosynthesis of flavonoids not only in a concentration-dependent manner but also in a time-dependent manner. The total flavonoid content reached a maximum at 24 h after SA treatment, which was 118.29% higher than the control. Furthermore, the biomass reached maximum values at 24 h and 36 h, which were 26.11% and 23.76% higher than the control, respectively. The total flavonoid content could be increased up to 15.02 μg rutin equivalents per mg mushroom biomass with the optimum conditions determined by response surface methodology. In this treatment, the biomass was also increased by 26.48%. This approach provides an efficient strategy for improving flavonoid accumulation in Ph. igniarius, with potential value in other applications.