Background: Hypertrophic obstructive cardiomyopathy (HOCM) is a serious and complex chronic disease severely affecting patients’ daily lives and health-related quality of life (HRQoL). The psychometric performance of generic preference-based instruments has not been compared in Chinese patients with HOCM. We aimed to identify an applicable vehicle to determine HRQoL and explore the psychometric properties of SF-6Dv2 and EQ-5D-5L in adults with HOCM. The interchangeability of the tools in cost-utility analysis was also investigated. Methods: We collected data from 131 patients with HOCM from the First Affiliated Hospital of Zhengzhou University, China. Assessments were performed on the day of admission and three and six months after discharge using SF-6Dv2 and EQ-5D-5L. The responses were converted to utility values using the corresponding Chinese value sets. The tool distributions were explored, and the floor and ceiling effects were analyzed. The agreement was assessed using intra-class correlation coefficients (ICCs) and Bland–Altman plots. Convergent validity was tested using Spearman’s rank correlation coefficient. Known group validity was measured across various clinical and sociodemographic indicators using relative efficiency (RE) statistics. Results: The mean utility scores for SF-6Dv2 and EQ-5D-5L at baseline and 6-month follow-up were 0.61, 0.62, 0.736, and 0.797, respectively. The EQ-5D-5L and SF-6Dv2 distribution scores showed no normality. EQ-5D-5L was more sensitive to changes over time and showed a moderate to good correlation with the SF-6Dv2 (ICC: 0.598–0.862). The instruments’ agreement and convergent validity worsened in patients with a higher New York Heart Association (NYHA) cardiac function classification and lower general health status. SF-6Dv2 showed higher relative efficiency statistics and a greater ability to distinguish external health status. Conclusions: The measured results can be used for future cost-utility analyses. SF-6Dv2 and EQ-5D-5L presented different results and should not be used interchangeably. SF-6Dv2 is optimal for detecting differences between subgroups with various health states.