The objective of this study was to investigate the expression of SVEP1 in hepatocellular carcinoma (HCC) and to evaluate the association among SVEP1, cancer stem cell-like phenotype, and the prognosis of patients to provide new possibilities for the accurate diagnosis and stratification of HCC. Two hundred HCC and paired adjacent tissues were analyzed by immunohistochemistry and scored, and their relationships with clinicopathological parameters and survival rates were analyzed. We found that compared with adjacent tissues, the expression of SVEP1 in HCC was relatively low and was closely related to tumor size, satellite nodule formation, and histological grade (p<0.05). Statistical analysis showed that the survival rate of patients with low expression of SVEP1 decreased significantly (p<0.05). Our results showed that the expression of SVEP1 was negatively correlated with the expression of the cancer stem cell markers CD44 and CD133 (p<0.05). Moreover, multivariate Cox regression analysis showed that SVEP1 was an independent prognostic factor for the survival of HCC patients. In conclusion, our results suggest that decreased SVEP1 expression may promote HCC acquisition of a cancer stem cell-like phenotype, ultimately leading to heterogeneity and poor prognosis of HCC. This work may provide new insight into the development of HCC and suggests a potential marker for predicting the prognosis of patients.