Patients with obstructive hypertrophic cardiomyopathy (HOCM) have large papillary and trabecular muscles (PTMs), which are myocardial tissue. PTMs are usually excluded from the myocardium and included in the left ventricular (LV) cavity when determining LV mass (LVM) and volumes using cardiac magnetic resonance (CMR). This conventional method may result in large distortion of LVM and other indices. We investigated 74 patients with HOCM undergoing CMR imaging. LV short-axis cine images were obtained. LV contours were drawn using two different methods: (1) the conventional method, where PTMs were included in the LV cavity; and (2) the mask method, which includes the TPMs in the LV myocardium. The LV end-diastolic volume (LV-EDV), LV end-systolic volume (LV-ESV), LV ejection fraction (LVEF), and the LVM were then calculated. Fasting NT-proBNP and CK-MB levels were measured with ELISA. In patients with HOCM, mass of PTMs (MOPTM) was 47.9 ± 18.7 g, which represented 26.9% of total LVM. Inclusion of PTMs with the mask method resulted in significantly greater LVM and LVM index (both p < 0.0001) in comparison with those measured with the conventional method. In addition, the mask method produced a significant decrease in LV-EDV and LV-ESV. LVEF was significantly increased with the mask method (64.3 ± 7.9% vs. 77.2 ± 7.1%, p < 0.0001). MOPTM was positively correlated with BMI, septal wall thickness, LVM, LV-EDV, and LV-ESV. LVEF was inversely correlated with MOPTM. In addition, MOPTM correlated positively with NT-proBNP (r = 0.265, p = 0.039) and CK-MB (r = 0.356, p = 0.002). In conclusion, inclusion of PTMs in the myocardium has a substantial impact on quantification of the LVM, LV-EDV, LV-ESV, and LVEF in patients with HOCM. The effects of the PTMs in women was greater than that in men. Furthermore, the MOPTM was positively associated with NT-proBNP and CK-MB. The PTMs might be included in the myocardium when measuring the LV volumes and mass of patients with HOCM. At present, the clinical and prognostic meaning and relevance of the PTMs is not clear and should be further studied.