Rhizoma Atractylodis macrocephalae have an important role in treating cerebrovascular diseases in Traditional Chinese Medicine (TCM). The purpose of the present study was to determine the neuroprotective effect of Atractylodis macrocephalaon polysaccharides (AMPS) on hypoxia-induced apoptosis of cerebral cortical neurons. Neuronal cells obtained from neonatal rats were divided into the following groups: Normal control (group C); apoptosis positive induced by hypoxia-reoxygenation culture of rat primary cerebral cortical neurons (group A); treated with 0.025 g/l AMPS prior to hypoxia culture of neurons (AMPS1); treated with 0.05 g/l AMPS (AMPS2); treated with 0.1 g/l AMPS (AMPS3); and treated with 0.25 g/l AMPS (AMPS4). Neuronal apoptosis was examined with Annexin V-fluorescein isothiocyanate/propidium iodide, Hoechst 33342 fluorescent staining, Rhodamine 123 staining, polymerase chain reaction assay and immunocytochemical staining. The results showed that the AMPS significantly prevented the growth inhibition, mitochondrial injury and apoptosis of neurons induced by hypoxia. The levels of Caspase-3 and Bax mRNAs and proteins were significantly downregulated by AMPS in neurons exposed to hypoxia, and the levels of B-cell lymphoma 2 (Bcl-2) protein was significantly upregulated by AMPS in neurons exposed to hypoxia, as compared with group A (P<0.05). The ratio of Bcl-2/Bcl-2-associated X protein (Bax) mRNA and protein was significantly increased by AMPS in neurons exposed to hypoxia as compared with group A (P<0.05). The observed improved neuronal growth and inhibition neuronal apoptosis by AMPS may be due to a decrease in the levels of Bax and Caspase-3 and an increase in the levels of Bcl-2 and the ratio of Bcl-2/Bax in hypoxic neurons.