This study aimed to identify the phenotypic features contributing to the development of left ventricular outflow tract obstruction (LVOTO) in patients with hypertrophic cardiomyopathy (HCM) and to evaluate the genotype‒phenotype relationship. This cross-sectional study included 96 patients diagnosed with HCM (mean age: 56.9 ± 13.5 years, 32.3% female). The patients were divided into hypertrophic nonobstructive cardiomyopathy (HNCM; n = 60) and hypertrophic obstructive cardiomyopathy (HOCM; n = 36) groups. All patients underwent CMR. Patients (n = 77) who had previously provided formal approval underwent a genetic examination that included 18 genes. The anterior mitral leaflet (AML) length/LVOT diameter ratio, posterior mitral leaflet (PML) length/LVOT diameter ratio, and anterolateral papillary muscle (AL-PM) mobility were associated with LVOTO, independent of the basal IVS thickness, abnormal chordal attachment, and bifid PM. An AML length/LVOT diameter ratio of ≥ 2.30, a PML length/LVOT diameter ratio of ≥ 1.83, and an AL-PM mobility of ≥ 57.7% were predictors of LVOTO, with good sensitivity and specificity. Positive variants (VUS, LP, and P) were detected in 37.7% (29 of 77) of the patients who underwent genetic testing. The LP/P variant was detected in 20.8% (16 of 77) of patients. Three groups (variant-negative, VUS, and LP/P groups) had significant differences in the LVOT diameter (median 14, 12, and 10 mm, respectively; p = 0.021), AML length (mean 25.3, 26.5, and 27.5 mm, respectively; p = 0.029), AML length/LVOT diameter ratio (median 1.74, 2.33, and 2.85, respectively; p = 0.006), PML length/LVOT diameter ratio (median 1.29, 1.82, and 2.10, respectively; p = 0.045), and abnormal chordal attachment (6.3%, not observed, and 31.3%, respectively; p = 0.009). The AML length/LVOT diameter ratio, PML length/LVOT diameter ratio, and AL-PM mobility were associated with LVOTO. In addition, genetic testing results may provide information regarding the phenotypic expression of patients with HCM.