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Higher levels of serum alkaline phosphatase (ALP) as a novel risk factor was recently found associated with mortality in different population, whereas, the relationship remains unknown in hypertrophic cardiomyopathy (HCM) population. In this study, we hypothesized that increased ALP could predict all-cause mortality in the adult HCM population. In this cohort study, retrospective data from 538 HCM patients consecutively recruited in West China Hospital were collected. Patients were divided into two groups by baseline ALP with 80 IU/L as the cutoff. All-cause mortality was set as the endpoint. Subgroup analysis was conducted in patients with normal liver function. In total, 461 adult HCM patients were included. After a median follow-up of 4.7 years, 91 patients died. Alkaline phosphatase was an independent predictor of all-cause mortality since patients in the higher ALP group had an increased risk (adjusted HR 2.0, 95% CI: 1.3-3.3, P < 0.01) compared with those in the lower ALP group. In subgroup analysis, the relationship was consistent with the overall (adjusted HR: 3.0, 95% CI: 1.7-5.3, P < 0.01 for the higher ALP group). In the Chinese cohort study of HCM patients, serum ALP is independently associated with all-cause mortality. Patients with a measured value above 80 IU/L had an increased risk of all-cause mortality and this cutoff might help with risk stratification in HCM population. [ABSTRACT FROM AUTHOR]