Background Hypertrophic cardiomyopathy (HCM) is a genetic disorder affecting not only the myocardium but also the mitral valve (MV) and its apparatus. This study aimed to investigate the prognostic implication of MV disease and its progression in East Asian patients with HCM. Methods and Results We assessed MV structure and function on the indexed echocardiogram of 1185 patients with HCM (mean±SD age, 60±14 years; men, 67%) in a longitudinal HCM registry, and 667 patients who performed follow‐up echocardiogram after 3 to 5 years were also analyzed. Progression of mitral regurgitation (MR) was defined as the increase of at least 1 grade. Clinical outcomes were defined as a composite of cardiovascular death, heart failure hospitalization, MV surgery or septal myectomy, and heart transplantation. Most of the entire cohort was nonobstructive type (n=1081 [91.2%]). A total of 278 patients (23.5%) showed at least mild MR on indexed echocardiogram. MR, systolic anterior motion, and mitral annular calcification were more prevalent in patients with obstructive HCM. During 7.0±4.0 years of follow‐up, presence of MR was independently associated with poor clinical outcomes (hazard ratio [HR], 1.60 [95% CI, 1.07–2.40]; P =0.023). On follow‐up echocardiogram, 67 (10.0%) patients showed MR progression, and it was independently associated with poor prognosis (HR, 2.46 [95% CI, 1.29–4.71]; P =0.007). Conclusions In East Asian patients with HCM whose major type is nonobstructive, MV disease is common. MR, systolic anterior motion, and mitral annular calcification are more prevalent in patients with obstructive HCM. The presence and progression of MR are associated with a poor prognosis in patients with HCM.