We here studied the clinical features, cardiac structure, and functional changes and prognosis of hypertrophic cardiomyopathy (HCM) patients with hypertension (HTN). A total of 90 HCM patients with HTN and 172 patients without HTN were divided into a hypertensive group and non-hypertensive group. The clinical characteristics, cardiac structure and function, and prognosis of the two groups were compared. Our study found that HCM patients with HTN had fewer syncope events in their medical histories (8% vs. 22%, P < 0.01) and sudden deaths in the family (3% vs. 10%, P < 0.05). The prevalence of apical hypertrophy (18% vs. 7%, P < 0.01) and midventricular obstruction (26% vs. 15%, P < 0.05) was higher in the HTN group. Besides, simple HCM patients had more pathogenic gene mutations, while those with HTN were more likely to have mutations of uncertain clinical significance (64% vs. 24%, P < 0.05). Evaluation of 5-year survival rate showed a trend for a worse prognosis in HCM patients with HTN, but the results were not statistically insignificant (P = 0.065). In conclusion, we found that the clinical phenotypes of HCM patients with HTN differed from those of patients with HCM alone, suggesting that HTN may play a pathogenic role in the pathogenesis of hypertensive hypertrophic cardiomyopathy patients.