In this work, a new type of complex was constructed by coordinating quercetin (QC) with cerium (Ce) ions. This complex was introduced into perfluorosulfonic acid resin (PFSA) to fabricate a proton exchange membrane. The coordination process prevented the formation of ion cross-links between cerium and sulfonic acid groups in PFSA, thereby keeping proton conductivity and fuel cell performance of membrane samples at a high level. Due to the insolubility of quercetin in water, its coordination with cerium minimized cerium migration, providing long-lasting resistance to free radicals. The effects of additives on PFSA membrane properties were investigated by measuring IEC, water uptake, swelling ratio, and proton conductivity. Fenton degradation experiments and membrane electrode assembly performance tests was conducted simultaneously. The results demonstrated that compared to the addition of quercetin or cerium alone, the use of QC-Ce increased the proton conductivity by 23.70% after 24-h Fenton degradation and lowered fluoride release by 58.29%. Meanwhile, the PFSA/QC-Ce composite membrane samples maintained an open circuit voltage of 0.935 V and a maximum power density of 668.15 mW cm−2 after 96 h of open circuit voltage hold testing.