Five undescribed caffeoylquinic acid derivatives (CQAs), along with fifteen known CQAs, were isolated from the roots of Arctium lappa L.(burdock). The chemical structures of compounds were determined using extensive spectroscopic analyses, including UV, IR, NMR and MS. Further in vitro bioactive investigation demonstrated the neuroprotective effects of these compounds against the neurotoxicity of hydrogen peroxide (H2O2) and N-methyl-D-aspartate (NMDA). 1,3,5-tri-O-caffeoylquinic acid and 1,4,5-tri-O-caffeoylquinic acid significantly reduced H2O2-induced human neuroblastoma SH-SY5Y cell death with concentration for 50% of maximal effect (EC50) values of 17.3 and 19.3 μM. Meanwhile, 3,5-di-O-caffeoyl-1-O-maloylquinic acid displayed protective effect against NMDA-induced cell injury with EC50 values of 18.4 μM. Overall, the more caffeoyl, the better the antioxidant activity, while the maloyl-containing compounds had better anti-NMDA activity.