Ischemic stroke (IS) is one of the most common neurological disease worldwide today. The risk factors of IS, such as hypertension, diabetes, obesity, aging, and formation of thrombus and atheromatous plaque, are demonstrated to be able to lead to poor prognosis of patients. The gut microbiota has attracted more attention in recent years, and the study focused on microbiota-gut-brain axis might help to reveal the mechanisms of the neurological and new therapeutic targets of IS. The microbiota-gut-brain axis describes the crosstalk between the gut microbiota, intestine, and center nervous system. At present, an increasingly number of studies have started to focus on the correlation between gut microbiota and risk factors of IS, indicating that the microbiota-gut-brain axis plays an important role in the pathogenesis of IS. This article reviews studies of how the gut microbiota alterations affect the progression of these risk factors, and how the onset of the risk factors would change the composition of gut microbiota. The primary purpose of the current study is to provide more comprehensive perspectives and collective ideas, in order to encourage more potential treatment for IS based on the microbiota-gut-brain axis.