In this study, two proteins with antioxidant activity, WLZP1F1G2 and WLZP1F1G3, were firstly isolated from the shell of Arca inflata, one source of Walengzi, a traditional Chinese medicine. This study used a green, traditional decoction extraction method coupled with column chromatography technique for protein extraction and purification. The protein types were determined by comparing their amino acid sequences from the transcriptome database of A. inflata. Then, a number of techniques including UV, FT-IR, circular dichroism, scanning electron microscopy and atomic force microscopy were used to characterize the structural properties of WLZP1F1G2 and WLZP1F1G3. WLZP1F1G2 was a type of ferritin while WLZP1F1G3 was a type of promyosin. They both shown good temperature stability and pH tolerance. WLZP1F1G2 and WLZP1F1G3 were tested for their antioxidant capacity in both in vitro and in vivo experiments. They all had good ability to clear ABTS, DPPH, and oxygen free radicals. And they all showed good Fe2+ chelating properties. Additionally, in vivo tests on wild-type Caenorhabditis elegans revealed that WLZP1F1G2 and WLZP1F1G3 both had effective anti-aging properties. These results raised the possibility that WLZP1F1G2 and WLZP1F1G3 could function as food preservatives and antioxidants. Display omitted •Proteins were extracted from Walengzi using a green and environmental friendly method.•Amino acid sequences of WLZP1F1G2 and WLZP1F1G3 were identified by LC-MS/MS.•WLZP1F1G2 and WLZP1F1G3 could clear free radicals related to aging in vivo.•WLZP1F1G2 and WLZP1F1G3 had certain anti-aging activity in Caenorhabditis elegans.•WLZP1F1G2 and WLZP1F1G3 were promising antioxidants.