Microvascular invasion (MVI) is regarded as one of the independent risk factors for recurrence and poor prognosis of hepatocellular carcinoma (HCC). The presence of MVI in HCCs was evaluated on the basis of pathological reports of surgical specimens and was defined as tumor within a vascular space lined by endothelium that was visible only on microscopy. The aim of the study was to investigate the usefulness of intravoxel incoherent motion (IVIM) diffusion weighted (DW) magnetic resonance (MR) imaging in predicting MVI of HCC. Preoperative IVIM DW imaging and Gd-EOB-DTPA-enhanced MRI (DCE-MRI) of 51 patients were analyzed. Standard apparent diffusion coefficient (ADC), D (the true diffusion coefficient), D* (the pseudodiffusion coefficient) and f (the perfusion fraction), relative enhancement (RE) and radiological features were evaluated and analyzed. Univariate analysis revealed that HCCs with MVI had a higher portion of an irregular tumor shape than HCCs without MVI (p = 0.009), the Standard ADC, D value were significantly lower in HCCs with MVI (p = 0.022, p = 0.007, respectively). Multivariate analysis revealed that an irregular shape (p = 0.012) and D value ≤ 1.16×10-3mm2/sec (p = 0.048) were independent predictors for MVI. Combining the two factors of an irregular shape and D value, a sensitivity of 94.4% and specificity of 63.6% for predicting MVI was obtained. In conclusion, we found that an irregular shape and D value ≤ 1.16×10-3mm2/sec may suggest the presence of MVI in HCCs.