Background: Hypertrophic obstructive cardiomyopathy (HOCM) patients are reported to have a potential risk of sudden cardiac death (SCD); however, HCM with left ventricular outflow tract (LVOT) obstruction, which is regarded as a risk indicator of SCD, is doubtful since the LVOT gradient is dynamic and may be confounded by various environmental factors and routine activities. The purpose of this study was to explore the clinical prognosis of HOCM through a multicenter cohort study with data-driven propensity score matching (PSM) analysis. Methods: The cohort included 2268 patients with HCM from 1996 to 2021 in 13 tertiary hospitals. In the present study, we excluded 458 patients who underwent alcohol septal ablation (ASA) and septal myectomy (SM) surgery so 1810 HCM patients were eventually included. We developed a data-driven propensity score using 24 demographic and clinical variables to create 1:1 propensity-matched cohorts. A Cox proportional hazard regression model was constructed to assess the effect of HOCM on mortality. Results: After logit-matching, there were no significant differences in all-cause mortality (log-rank \chi{}^2 = 1.509, p = 0.22), cardiovascular mortality/cardiac transplantation (log-rank \chi{}^2 = 0.020, p = 0.89) or SCD (log-rank \chi{}^2 = 0.503, p = 0.48) between patients with HOCM and hypertrophic nonobstructive cardiomyopathy (HNCM), and according to the Cox proportional hazard regression model, LVOT obstruction was not a risk predictor in patients with HCM. Conclusions: In both matched and unmatched cohorts, there were no significant differences in clinical prognosis between HOCM and HNCM patients, and LVOT obstruction was not an independent risk predictor of prognosis in patients with HCM. Clinical Trial Registration: ChiCTR1800017330.