This work reports the isolation of seven undescribed polyphenolic glycosides (1−7) together with fourteen known compounds (8−21) from the fruit of Lycium ruthenicum Murray. The structures of the undescribed compounds were identified based on comprehensive spectroscopic methods including IR, HRESIMS, NMR and ECD, and chemical hydrolysis. Compounds 1−3 possess an unusual four-membered ring, while 11−15 were firstly isolated from this fruit. Interestingly, compounds 1−3 inhibited monoamine oxidase B with IC50 of 25.36 ± 0.44, 35.36 ± 0.54, and 25.12 ± 1.59 μM, respectively, and showed significant neuroprotective effect on PC12 cells injured by 6-OHDA. Moreover, compound 1 improved the lifespan, dopamine level, climbing behavior, and olfactory ability of the PINK1B9 flies, a Drosophila model of Parkinson's disease. This work presents the first in vivo neuroprotective evidence of the small molecular compounds in L. ruthenicum Murray fruit, indicating its good potential as neuroprotectant.