Using noninvasive radiomics to predict pathological biomarkers is an innovative work worthy of exploration. This retrospective cohort study aimed to analyze the correlation between NAD(P)H quinone oxidoreductase 1 (NQO1) expression levels and the prognosis of patients with hepatocellular carcinoma (HCC) and to construct radiomic models to predict the expression levels of NQO1 prior to surgery. Data of patients with HCC from The Cancer Genome Atlas (TCGA) and the corresponding arterial phase-enhanced CT images from The Cancer Imaging Archive were obtained for prognosis analysis, radiomic feature extraction, and model development. In total, 286 patients with HCC from TCGA were included. According to the cut-off value calculated using R, patients were divided into high-expression (n = 143) and low-expression groups (n = 143). Kaplan-Meier survival analysis showed that higher NQO1 expression levels were significantly associated with worse prognosis in patients with HCC (p = 0.017). Further multivariate analysis confirmed that high NQO1 expression was an independent risk factor for poor prognosis (HR = 1.761, 95% CI: 1.136-2.73, p = 0.011). Based on the arterial phase-enhanced CT images, six radiomic features were extracted, and a new bi-regional radiomics model was established, which could noninvasively predict higher NQO1 expression with good performance. The area under the curve (AUC) was 0.9079 (95% CI 0.8127-1.0000). The accuracy, sensitivity, and specificity were 0.86, 0.88, and 0.84, respectively, with a threshold value of 0.404. The data verification of our center showed that this model has good predictive efficiency, with an AUC of 0.8791 (95% CI 0.6979-1.0000). In conclusion, there existed a significant correlation between the CT image features and the expression level of NQO1, which could indirectly reflect the prognosis of patients with HCC. The predictive model based on arterial phase CT imaging features has good stability and diagnostic efficiency and is a potential means of identifying the expression level of NQO1 in HCC tissues before surgery.