Objective In order to investigate the mechanism of hypoxia damage in which the hypoxia-induced- microglia activation acts to hippocampal neurons, the indirect co-culture system was established by using the culture medium which had already trained by microglia cell N9 then used to cultivate fetal rat hippocampal neurons. Methods The co-culture system was established. The neuron growth and Caspase-3 activity of different groups were explored by TUNEL method and chemiluminescence. The expression levels of NO, OSUB>2/SUB>SUP>-/SUP> and TNF-α in different group were detected by immunofluorescence, Griess reagent method, WST-1 method and ELISA method. Results In N9 cells culture medium after 12 hours hypoxia the proliferation, vitality and apoptosis of neuron of conventional cultured and hypoxia cultured were inhibited. The stress-induced neurotoxic factors, NO, OSUB>2/SUB>SUP>-/SUP> and TNF-α in the altogether hypoxic culture system have the highest level than those in the pure culture and conventional co-culture system. Conclusion Microglia activation plays an important role in hypoxia-induced neuronal damage. The effector molecule is the neurotoxic molecule pr