Microglial cells are phagocytic cells of the central nervous system (CNS) and have been proposed to be a primary component of the innate immune response and maintain efficient CNS homeostasis. Microglial cells are activated during various phases of tissue repair and participate in various pathological conditions in the CNS. Following spinal cord injury (SCI), anoxemia is a key problem that results in tissue destruction. Hypoxia-inducible factor 1-alpha (HIF-1 alpha) may protect hypoxic cells from apoptosis or necrosis under ischemic and anoxic conditions. However, numerous studies have revealed that hypoxia upregulates HIF-1 alpha expression leading to the death of microglial cells. The present study investigated the alterations in HIF-1 alpha expression levels and the mechanism of autophagic cell death mediated by HIF-1 alpha in microglial cells induced by hypoxia. Hypoxia was demonstrated to induce HIF-1 alpha expression and autophagic cell death in microglial cells. Enhanced autophagy reduced cell death during the initial stages by restraining the functions of autophagy-associated genes (microtubule-associated protein 1A/1B-light chain 3 phosphatidylethanolamine conjugate and Beclin-1) and modulating the expression of inflammatory cytokines (tumor necrosis factor-alpha and interleukin-1 beta). Target value was determined by Cell Counting Kit 8 and cell death by flow cytometry. Transmission electron microscopy, immunohistochemical staining, reverse transcription-quantitative polymerase chain reaction, western blotting, and ELISA were used for further analysis. However, increased expression of HIF-1 alpha induced cell death and autophagic cell death in microglial cells. Furthermore, the effects of the HIF-1 alpha inhibitor 2-methoxyestradiol and HIF-1 alpha small interfering RNA on the death and autophagy of microglial cells in vitro were investigated. These investigations revealed the suppression of autophagy, the decrease of cell viability and the increase of inflammatory cytokines results from HIF-1 alpha inhibition or HIF-1 alpha silencing. In conclusion, the results indicated that appropriate expression of HIF-1 alpha can ameliorate autophagic cell death of microglial cells associated with hypoxia, and may provide a novel therapeutic approach for SCI associated with microglial cell activation.