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Objective To explore the relationship between phenotypic changes of retinal microglia and retinal ganglion cells (RGCs) death after optic nerve injury. Methods Male C57BL/6J mice (6 to 8 weeks old) were randomly divided into 1-, 3-, 7-, and 14-day injury groups and sham operation group, with 4 mice in each group. The eyes in the injured groups were inflicted with optic nerve crush (ONC), while the eyes of the sham operation group were treated with the same operation procedure but without optic nerve clamp. Flash visual evoked potential (fVEP) and immunofluorescence staining were employed to evaluate the impact of optic nerve injury on visual function and number of RGCs. RT-qPCR and immunofluorescence staining were applied to detect the effecy of optic nerve injury on phenotypic changes in retinal microglia. Results fVEP results showed that the visual conduction of the injured eye was gradually decreased over time when compared with that of the sham group (P < 0.01). Immunofluorescence staining revealed that the number of RGCs was lost mainly within 7 d after injury (P < 0.01). At the same time, the number of retinal microglia reached its peak at 7 d after injury (P < 0.01). RT-qPCR indicated that the expression of disease-associated microglia (DAM) and interferon-responsive microglia (IRM) specific genes were significantly increased when compared with the sham group at 7 d after ONC (P < 0.01). Immunofluorescence staining displayed that the number of DAM peaked at 3 d after ONC (P < 0.01), but the proportion was decreased gradually with the progress of time (P < 0.05). The number and proportion of IRM peaked 7 d after ONC (P < 0.01). Correlation analysis suggested that the number of IRM was strongly correlated with the loss of ganglion cells (P < 0.01). Conclusion The conversion of retinal microglia from DAM type to IRM type after optic nerve injury may be an important cause of ganglion cell loss.