Introduction: With a prevalence of up to 1 in 200, hypertrophic cardiomyopathy (HCM) is the most common monogenic hereditary cardiovascular disease. Previous studies have observed that mitochondrial dysfunction and mitochondria-associated metabolic remodeling are major metabolic features in HCM. However, the impact of mitochondrial gene mutations on HCM were poorly understood. Methods and Results: We selected 2272 mitochondrial genes from the Mitocarta database 3.0 and screened rare variants from the whole-exome sequencing data in 985 HCM patients (excluding patients with HCM phenotypes, including mitochondrial myopathy) and 759 non-HCM controls. We found that CYP2E1 rare variants were significantly enriched in HCM patients (OR = 9.56, Bonferroni corrected P = 0.001). Patients with or without CYP2E1 rare variants shared similar demographic and echocardiographic variables at baseline. With a median follow-up time of 5.31 years in 735 HCM patients, we revealed that HCM patients with CYP2E1 rare variants were more likely to experience myocardial infarction (HR 14.1, P < 0.001). Conclusion: We demonstrated that rare variants in the mitochondrial gene CYP2E1 might increase the risk of HCM onset and may be associated with the occurrence of myocardial infarction endpoints in HCM. We hypothesize that the mechanism is related to the extensive and complex mitochondrial metabolic processes in which CYP2E1 is involved. Our findings provided new evidence for the association between mitochondrial gene variants and HCM, and more multi-center evidence is needed to confirm this association in the future.