The study aimed to evaluate the changes of left ventricular diastolic function and the improvement of clinical symptoms in hypertrophic cardiomyopathy (HCM) patients with heart failure with preserved ejection fraction (HFpEF) after percutaneous intramyocardial septal radiofrequency ablation (PIMSRA). This study enrolled 31 adult HCM patients with HFpEF who underwent PIMSRA treatment. Electrocardiogram, imaging, and blood biochemical examinations were performed on these patients during a 6-month follow-up. Compared with the baseline, at 6 months after PIMSRA, patients showed significant reductions in peak left ventricular outflow tract pressure gradients (resting gradient: from a mean of 83.24 to 23.40mmHg, p < 0.001; postexercise gradient: from a mean of 109.70 to 33.39mmHg, p< 0.001). The interventricular septal thickness reduced from a mean of 22.90 to 17.48mm, p < 0.001. The E/e' decreased from a median of 18.67 to 11.54, p < 0.001. The 6-minute walk distance (6MWD) increased from a mean of 359.03 to 435.81 m, p < 0.001. The Kansas City Cardiomyopathy Questionnaire Overall Summary Score (KCCQ OS) increased from a mean of 57.57 to 71.93, p < 0.001. The number of HFpEF patients diagnosed according to the European Society of Cardiology's Heart Failure Association HFA-PEFF score decreased from 31 to 23. None of the patients had new-onset bundle branch block or complete heart block after PIMSRA. PIMSRA is a safe and effective treatment. It can improve left ventricular diastolic function and quality of life in HCM patients.