INTRODUCTION: H-type hypertension (HHTN) is a subtype of hypertension that tends to worsen the prognosis of acute ischemic stroke (AIS). Recent studies have highlighted the vital role of gut microbiota in both hypertension and AIS, but there is little available data on the relationship between gut microbiota and the progression of AIS patients with HHTN. In this study, we investigated the microbial signature of AIS patients with HHTN and identified characteristic bacteria as biomarkers for predicting prognosis. METHODS: AIS patients with HHTN ( = 150) and without HHTN ( = 50) were enrolled. All patients received a modified Rankin Scale (mRS) assessment at 3 months after discharge. Fecal samples were collected from the participants upon admission, including 150 AIS patients with HHTN, 50 AIS patients with non-HHTN, and 90 healthy subjects with HHTN. These samples were analyzed using 16S rRNA sequencing to characterize the bacterial taxa, predict functions, and conduct correlation analysis between specific taxa and clinical features. RESULTS: Our results showed that the composition of the gut microbiota in HHTN patients differed significantly from that in non-HHTN patients. The abundance of the genera , , , , and in AIS patients with HHTN was significantly increased compared to AIS patients without HHTN, while the genus , , and were significantly decreased. Moreover, , , , and in AIS patients with HHTN were more abundant than healthy subjects with HHTN, while , , and were less abundant. Moreover, the genera , and were negatively connected with the NIHSS score, and the genera and were observed to be negatively associated with the mRS score. The genera , , and were associated with a poor prognosis, whereas the increase in and was correlated with good outcomes. Generated by eight genera and clinical indexes, the area under the curve (AUC) value of the receiver operating characteristic (ROC) curve achieved 0.739 to effectively predict the prognosis of AIS patients with HHTN. CONCLUSION: These findings revealed the microbial signature of AIS patients with HHTN and further provided potential microbial biomarkers for the clinical diagnosis of AIS patients with HHTN.