To investigate the value of the combined application of intravoxel incoherent motion (IVIM) and enhanced T2*-weighted angiography (ESWAN) for preoperative prediction of microvascular invasion (MVI) in hepatocellular carcinoma (HCC). 76 patients with pathologically confirmed HCC were retrospectively enrolled and divided into the MVI-positive group (n=26) and MVI-negative group (n=50). Conventional MRI, IVIM, and ESWAN sequences were performed. Three region of interests (ROIs) were placed on the maximum axial slice of the lesion on D, D*, and f maps derived from IVIM sequence, and R2* map derived from ESWAN sequence, and intratumoral susceptibility signal (ITSS) from the phase map derived from ESWAN sequence was also automatically measured. Receiver operating characteristic (ROC) curves were drawn to evaluate the ability for predicting MVI. Univariate and multivariate logistic regression were used to screen independent risk predictors in clinical and imaging information. The Delong's test was used to compare the differences between the area under curves (AUCs). The D and D* values of MVI-negative group were significantly higher than those of MVI-positive group (P=0.038, and P=0.023), which in MVI-negative group were 0.892×10-3 (0.760×10-3, 1.303×10-3) mm2/s and 0.055 (0.025, 0.100) mm2/s, and in MVI-positive group were 0.591×10-3 (0.372×10-3, 0.824×10-3) mm2/s and 0.028 (0.006, 0.050)mm2/s, respectively. The R2* and ITSS values of MVI-negative group were significantly lower than those of MVI-positive group (P=0.034, and P=0.005), which in MVI-negative group were 29.290 (23.117, 35.228) Hz and 0.146 (0.086, 0.236), and in MVI-positive group were 43.696 (34.914, 58.083) Hz and 0.199 (0.155, 0.245), respectively. After univariate and multivariate analyses, only AFP (odds ratio, 0.183; 95% CI, 0.041-0.823; P = 0.027) was the independent risk factor for predicting the status of MVI. The AUCs of AFP, D, D*, R2*, and ITSS for prediction of MVI were 0.652, 0.739, 0.707, 0.798, and 0.657, respectively. The AUCs of IVIM (D+D*), ESWAN (R2*+ITSS), and combination (D+D*+R2*+ITSS) for predicting MVI were 0.772, 0.800, and, 0.855, respectively. When IVIM combined with ESWAN, the performance was improved with a sensitivity of 73.1% and a specificity of 92.0% (cut-off value: 0.502) and the AUC was significantly higher than AFP (P=0.001), D (P=0.038), D* (P=0.023), R2* (P=0.034), and ITSS (P=0.005). The IVIM and ESWAN parameters showed good efficacy in prediction of MVI in patients with HCC. The combination of IVIM and ESWAN may be useful for noninvasive prediction of MVI before clinical operation.