Objective To explore the value of 3.0 T cardiac magnetic resonance (CMR) intravoxel incoherent motion (IVIM) for evaluating microvascular dysfunction in hypertrophic cardiomyopathy (HCM) patients. Methods Twenty-six HCM patients and 12 healthy controls, who received CMR examination in the First Hospital of Lanzhou University from Apr. 2016 to Oct. 2017, were enrolled. All volunteers underwent short-axis cardiac cine and IVIM scans, and HCM patients underwent late gadolinium enhancement (LGE) scan. The fraction of fast apparent diffusion coefficient (f), fast apparent diffusion coefficient (ADC_fast) and slow apparent diffusion coefficient (ADC_slow) were measured using MITK-Diffusion post-processing software. End-diastolic thickness (EDTH) was measured on short-axis cine image. HCM patients were grouped according to the severity of the left ventricular hypertrophy and whether having LGE or not. The differences of f value, ADC_fast and ADC_slow were compared between HCM patients and healthy controls, non-hypertrophic segments and hypertrophic segments of HCM patients, LGE segments and non-LGE segments of HCM patients, and different hypertrophic subgroups in hypertrophic segment group. Spearman correlation analysis was performed to explore the correlation between IVIM parameters (f value, ADC_fast and ADC_slow) and EDTH in each segment. Results The ADC_slow and ADC_fast of the HCM patients were lower than those of the healthy controls (ADC_slow:0.003[0.002, 0.005] mm²/s vs 0.004[0.002, 0.007] mm²/s, ADC_fast:0.046[0.025, 0.074] mm²/s vs 0.069[0.052, 0.086] mm²/s), and the differences were significant (Z=-2.434 and -7.268, both P<0.05). There was no significant difference in the f value between the HCM patients and healthy controls (P>0.05). The ADC_fast values of the non-hypertrophic segment group and the hypertrophic segment group in the HCM patients were 0.051 (0.029, 0.077) mm²/s and 0.027 (0.019, 0.052) mm²/s, respectively, which were both significantly lower than that of the healthy controls (Z=-5.505 and -8.144, both P<0.01). The f value and ADC_fast of the hypertrophic segment were significantly lower than those of the non-hypertrophic segment (0.444[0.080, 0.834] vs 0.735[0.302, 0.877] and 0.027[0.019, 0.052] mm²/s vs 0.051[0.029, 0.077] mm²/s, Z=-3.527 and -4.722, both P<0.01). There was significant difference in ADC_fast between the mild, moderate, severe and extremely severe hypertrophic segment subgroups (0.035[0.021, 0.061] mm²/s, 0.023[0.015, 0.038] mm²/s, 0.018[0.013, 0.025] mm²/s and 0.012[0.005, 0.055] mm²/s, respectively; H=9.769, P=0.021); however, pairwise comparison showed no significant differences (all P>0.05). The f value and ADC_fast of the segmental myocardia with LGE were significantly lower than those without LGE (Z=-2.704 and -2.143, P=0.007 and 0.032). Spearman correlation analysis showed that EDTH was significantly negatively correlated with f value and ADC_fast (r=-0.195 and -0.282, both P<0.01). Conclusion CMR IVIM technology can non-invasively and quantitatively reflect cardiac microvascular dysfunction in HCM patients. The severity of microvascular dysfunction is related to the severity of myocardial hypertrophy. Microvascular dysfunction is also present in non-hypertrophic and non-LGE myocardia.