Atrioventricular node ablation (AVNA) combined with His bundle pacing (HBP) are feasible, safe, and effective in patients with refractory atrial fibrillation (AF), however, the pacing parameters of sensing and capture threshold maybe sometimes unsatisfactory. Left bundle branch pacing (LBBP) provides obvious advantage in patients with conduction diseases at the distal His bundle for its better sensing, a lower and more stable capture threshold. Among hypertrophic cardiomyopathy (HCM) patients, AF is a common sustained arrhythmia, primarily caused by left atrial dilatation and remodeling. Few is known about the feasibility of electrophysiological performance, safety and clinical effectiveness of atrioventricular junction ablation (AVJA) combined with LBBP in patient with refractory AF and HCM. Here, we report a case of a 56-year-old woman suffering from refractory AF and HCM, however HBP was failed for its unsatisfactory sensing, a high and unstable capture threshold for her, therefore, ablation and LBBB were accepted by her to achieve better rate control. Improvement in symptoms, quality of life, and exercise capacity has been observed during the 1.5-year follow-up. To our knowledge, our case originally confirmed that the combination of AVJA and LBBP, without the defect of AVNA combined with HBP, is a better strategy with feasibility and safety for refractory AF patients with comorbidity of HCM, additionally, it may make LBBP more applicable and valuable among patients suffering from HCM meanwhile pace maker treatments are essential.