A method for treating hypertrophic cardiomyopathy (HCM) utilizes an RF ablation electrode needle system that has an RF ablation generator, and an electrode needle. The electrode needle is introduced to puncture within myocardium and to reach the hypertrophic area of the interventricular septum. The RF ablation generator is then turned on to implement single-point or multi-point ablation on the hypertrophic area of the interventricular septum, and then the RF electrode needle is withdrawn from the patient.