Resveratrol (RES) and its two natural analogues, 4,4′-dihydroxystilbene (DHS) and pinosylvin (PIN), are very important polyphenols and have attracted considerable pharmaceutical interest because of their diverse biological activities. However, their adverse effects on motor nerves and glioma cells have not been properly assessed. Herein, we surveyed the toxicity and analyzed the structure-activity relationship of these three polyphenols using transgenic zebrafish ( Danio rerio) and U87. Results indicated that, in zebrafish embryos, both DHS (1 and 10 μg/mL) with hydroxyl groups at the 4 and 4′ positions, and PIN (1 and 10 μg/mL) with hydroxyl groups at the 3 and 5 positions inhibited motor neuron growth more effectively than RES (1 and 10 μg/mL) with hydroxyl groups at the 3, 4′, and 5 positions, although their appearance is normal. Both the DHS- (10 μg/mL) and PIN (10 μg/mL) -treated groups significantly reduced the swimming distance of zebrafish compared with the RES (10 μg/mL) -treated group. In addition, DHS with the hydroxyl groups at the 4 and 4′ positions (0.002, 0.02, 0.2, 2, and 20 μM) inhibited U87 cell aggregation in a concentration-dependent manner; PIN with the hydroxyl groups at the 3 and 5 positions (0.002, 0.02, 0.2, 2, and 20 μM) promoted U87 cell aggregation in a concentration-dependent manner, while RES with three hydroxyl groups promoted U87 cell aggregation at concentrations from 0.2 to 2 μM. Taken together, DHS and PIN are more neurotoxic than RES. The position and number of hydroxyl groups significantly affected the ability of the polyphenols to aggregate into tumors in the U87 cell.