Microvascular invasion (MVI) is considered to be an important factor in the early invasion and metastasis of liver cancer, and the survival rate of patients with MVI is much lower than that of patients without MVI. Therefore, it is crucial to accurately predict the independent predictors of tumor thrombus formation. This study aimed to assess the risk factors for tumor thrombus grades in patients with hepatocellular carcinoma (HCC). Between August 2011 and December 2022, the data of 231 patients diagnosed with HCC were collected and divided into the following three groups: an MVI-negative group, an MVI-positive group, and a portal vein tumor thrombus (PVTT) group. Univariate analysis was used to compare the differences between the three groups in terms of clinical features, pathology, and imaging features. Multiple logistic regression analysis was used to analyze the risk factors associated with tumor thrombus grades, and the cutoff value was finally calculated by using the receiver operating characteristic (ROC) curve. The incidence of MVI and PVTT in the patients with HCC were 10.0% and 6.1%, respectively; univariate analysis revealed statistically significant differences in tumor diameter, alpha fetoprotein level, Ki-67 expression level, gender, tumor quantity, arteriovenous fistula, peritumoral enhancement, and satellite nodules among the three groups (P<0.05). Multiple logistic regression analysis showed that Ki-67 expression level, tumor diameter, and peritumoral enhancement were independent risk factors for tumor thrombus grades (P<0.05). The area under the curve (AUC) of Ki-67 expression level and tumor diameter was 0.713 [95% confidence interval (CI): 0.626-0.800] and 0.753 (95% CI: 0.669-0.837), respectively, and the AUC of the combination analysis was 0.805 (95% CI: 0.723-0.888), with a cutoff value of 17.5% and 4.1 cm, respectively (P<0.05). Tumor diameter, Ki-67 expression level, and peritumoral enhancement can be used as independent predictors of tumor thrombus in patients with HCC. The combination of tumor diameter and Ki-67 expression level can further improve diagnostic efficacy.