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The toxicity of paraquat (PQ), a bipyridine cationic herbicide, to the lung and kidney has been widely recognized, but the acute toxic effects of PQ on the nervous system have received little attention. The aim of this study was to explore changes in the phenotypic differentiation of microglia in rats caused by acute PQ exposure. We found that acute PQ exposure induced pyknosis, edema and apoptosis in substantia nigra neurons. The results of immunohistochemistry and western blotting showed that the number of activated microglia increased, the number of microglia branches decreased and the length became shorter in the early stage of exposure to 25 mg/kg PQ. We then compared the mean fluorescence intensity of iNOS and ARG1. In the early stage of acute 25 mg/kg PQ exposure, the number of M1 phenotypes of microglia increased; in contrast, in the early stage of acute 45 mg/kg PQ exposure, the number of M2 phenotypes of microglia increased. On the 69th day, the expression of iNOS and ARG1 increased in the 25 mg/kg and 45 mg/kg PQ exposure groups. In sum, changes in microglia phenotypic differentiation were related to exposure dose and exposure time.