Ethnopharmacological relevance: Zishen Yutai Pills (ZYP), a famous traditional Chinese patent medicine, has been widely applied to avoid recurrent miscarriage and treat threatened abortion. Polysaccharides of ZYP (ZYPPs) play an essential role in the theraprutic effects of ZYP. However, the complex compositions of ZYP and the complicated structure of ZYPPs have posed great challenges and barriers to the quality evaluation of ZYP. Aim of the study: To identify and characterize the ZYPPs for better quality control of ZYP, a reliable and valid quality control system was established in this study. Materials and methods: A multi-fingerprint profile strategy based on HPSEC-MALL-RID, FT-IR, and HPLC (complete acid digested fingerprint, partial acid digested fingerprint and enzymatically digested fingerprint) was established to identify and discriminate the chemical structure of ZYPPs. Besides, the purpose of revealing the relationships between structure and biological activity of ZYPPs, their chemical characteristics, in vitro antioxidant and anti-glycation activities were investigated and discussed. Results: The similarity evaluation of ZYPPs indicated ZYPPs from different batches showed a high similarity based on the correlation coefficient values of multi-fingerprints. Furthermore, ZYPPs exhibited remarkable antioxidant and antiglycation properties, which might be attributed to their molecular weights and the content of uronic acids. Conclusions: These results indicated that the multiple fingerprint technique was reliable and effective for the improvement of quality control of ZYPPs, suggesting the multiple fingerprint technique could also be potentially applied as a valid and feasible strategy to control the quality of polysaccharide-enriched herbal medicines.