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Cerebral infarction (CI) is associated with high rates of disability, mortality, and death in China, but its mechanism is unclear. Therefore, early diagnosis of CI and determining its mechanism are very important. Intestinal microecology is thought to be related to cardiovascular and cerebrovascular diseases. We hypothesized that intestinal microecology is also related to CI and that the intestinal microecology in the stool of CI patients differs from that in healthy people.Fecal samples of healthy subjects and CI patient (all n = 10) and we investigated the intestinal microecology of CI patient and healthy people stool by 16 seconds sequencing and analyzed relative abundance and diversity of microorganisms by unweighted pair-group method with arithmetic mean analysis (UPGMA) and principal co-ordinates analysis (PCoA). We also measured apolipoprotein E (ApoE) levels in the serum by ELISA assay and analyzed the correlation between ApoE and intestinal flora.We found that the relative structure and diversity of intestinal microecology was significantly different between the stools of CI patients and healthy people. At the class level, Gammaproteobacteria was increased and Bacteroidia was decreased in CI patient stool. We found a correlation between ApoE in the serum and Bacteroidia and Gammaproteobacteria species.We considered the intestinal flora can be used as an indicator of CI and the up-regulation of ApoE may be the potential mediate for intestinal microecology contribute to CI.