Background: Patients with hypertrophic cardiomyopathy (HCM) represents diverse symptoms, morphology, and cardiovascular events. Although myocardium metabolism in patients with HCM has been studied, it is not well elucidated. In this study, we assessed the association between biomarkers, heart failure-related findings, genetic mutations, and myocardium lipid metabolism in HCM patients using imaging mass spectrometry. Method: We prospectively enrolled patients with HCM in Hamamatsu University hospital from July 2020 to October 2022. All patients underwent endomyocardial biopsy and genetic analysis. Obtained myocardial specimens were analyzed using a desorption electrospray ionization source attached to a mass spectrometer. Differences among groups were statistically evaluated with the Fisher’s exact test and Mann-Whitney U test. Correlations between the two values were analyzed using Spearman’s correlation coefficient values. Results: A total of 31 Japanese patients were enrolled in this study. These patients included 18 (58.0%) women, and the mean age was 67.6 ± 10.6 years. Genetic analysis revealed that six (19.4%) patients had pathogenic or likely pathogenic variant. (Frequency of causal genes was as follows: MYBPC3 2 [6.5%], TNNI3 2 [6.5%], MYH7 1 [3.2%], and MYOZ2 1 [3.2%].) We divided the patients into two groups according to their median intensity of candidate molecule to reveal between group differences. The group of high lysophosphatidylethanolamine (LPE) showed lower N-terminal pro-brain natriuretic peptide (NT-proBNP) levels (330.0 [147.0-614.0] pg/mL vs. 933.0 [699.5-2576.5] pg/mL, P = 0.001). A correlation was observed between the intensity of LPE and the NT-proBNP levels (r = -0.455, P = 0.012). There was no association between the presence of genetic mutations and New York Heart Association class and LPE intensity. Conclusion: HCM patients with the high intensity of LPE in myocardial tissue had relatively low NT-proBNP levels.