When the level of reactive oxygen species (ROS) increases abnormally in the body, it damages tissue cells and is closely related to the occurrence of various chronic diseases. Antioxidant peptides (APs) are a class of active short peptides with antioxidant capacity, which have great research value. In this paper, two APs were designed and synthesized based on the structural features of APs: CHIWM (AP1) and CHCPWM (AP2). The reactive sites and activities of APs were analyzed using the quantum chemical density functional theory (DFT) method. The reactive sites are all located in the indolyl heterocycle of tryptophan residues, among which AP1 has a smaller energy gap and single point energy. Multiple free radical scavenging assays showed that AP1 and AP2 had stronger antioxidant activity than the positive control, glutathione (GSH). For scavenging DPPH free radicals, the IC50s values were 0.613 mg/mL and 0.606 mg/mL, respectively. In cellular assays, both AP1 and AP2 were able to scavenge ROS in the cells and attenuate cellular damage. In conclusion, AP1 and AP2 designed in this paper have good antioxidant activity and have the potential to be applied in the treatment of chronic diseases caused by cellular oxidative damage.