Penthorum chinense Pursh is rich in flavonoids, which have strong antioxidant and anticomplement activities. In order to optimize their extraction conditions, various extraction parameters were chosen to identify their effects on flavonoids extraction. Single factor and Box–Behnken experimental designs consisting of 24 experimental runs and five replicates at zero point were applied to obtain the optimal extraction yield. The optimization conditions for flavonoids extraction were determined as follows: ethanol concentration 60.89%, extraction time 68.15 min, temperature 52.89 °C and liquid/solid ratio 19.70 : 1. The corresponding flavonoids content was 7.19%. The regression equation was found to fit well with the actual situation. Furthermore, the antioxidant activity (the free radical scavenging ability and ferric reducing/antioxidant power) and anticomplement ability of the flavonoids from P. chinense were determined. Results showed that the flavonoids of P. chinense displayed significant antioxidant and anticomplement activities. Its antioxidant activity can compete with ascorbic acid (Vc), whereas its anticomplement activity (IC₅₀ = 111.6 μg ml⁻¹) surpassed the effect of heparin (IC₅₀ = 399.7 μg ml⁻¹) which was used as the positive control, suggesting that P. chinense flavonoids and their related products could potentially be used as a promising natural agent in the treatment of humoral effector inflammation.