This comprehensive study focused on evaluating and selecting seven distinct commercial membranes to develop BTESE/PA membranes. This method effectively facilitated the extraction of cynaroside from the complex composition of peony seed meal. We subsequently conducted a thorough investigation into its biological properties. These findings establish a robust foundation for future research and the development of related products. The peak concentration achieved by peony seed meal filtration (PSMF) was 234.84 ± 1.17 μg/mL. Among the commercial membranes evaluated, the PA membrane exhibited superior separation capabilities, leading to its selection for BTESE loading. Compared with BTESE treated with HCl and NH3, the HCl variant, once incorporated into the BTESE/PA membrane, enhanced cynaroside separation, achieving an impressive 90.23% recovery rate. A comprehensive investigation of the biological effects of cynaroside revealed its crucial antioxidant role, especially in SOD binding. Additionally, cynaroside has the potential to induce apoptosis in K562 cells through interactions with BCL‐2 and CDK‐2 enzymes. Pharmacophore screening revealed the affinity of cynaroside for the PDE5A, TNKS2, and DAPK1 proteins, suggesting that it has diverse potential applications.