The turbulent kinetic energy (TKE) estimation based on 4D flow MRI has been currently developed and can be used to estimate the pressure gradient. The objective of this study was to validate the clinical value of 4D flow-based TKE measurement in patients with hypertrophic cardiomyopathy (HCM). From April 2018 to March 2019, we recruited 28 patients with HCM. Based on echocardiography, they were divided into obstructed HCM (HOCM) and non-obstructed HCM (HNCM). Triple-velocity encoding 4D flow MRI was performed. The volume-of-interest from the left ventricle to the aortic arch was drawn semi-automatically. We defined peak turbulent kinetic energy (TKEpeak) as the highest TKE phase in all cardiac phases. TKEpeak was significantly higher in HOCM than in HNCM (14.83 ± 3.91 vs. 7.11 ± 3.60 mJ, P < 0.001). TKEpeak was significantly higher in patients with systolic anterior movement (SAM) than in those without SAM (15.60 ± 3.96 vs. 7.44 ± 3.29 mJ, P < 0.001). Left ventricular (LV) mass increased proportionally with TKEpeak (P = 0.012, r = 0.466). When only the asymptomatic patients were extracted, a stronger correlation was observed (P = 0.001, r = 0.842). TKE measurement based on 4D flow MRI can detect the flow alteration induced by systolic flow jet and LV outflow tract geometry, such as SAM in patients with HOCM. The elevated TKE is correlated with increasing LV mass. This indicates that increasing cardiac load, by pressure loss due to turbulence, induces progression of LV hypertrophy, which leads to a worse prognosis.