Background: Computed tomography angiography (CTA) is one of the most commonly used imaging technique for the management of vascular diseases. Here, we aimed to develop a hybrid method combining a feature-based expert system with a supervised deep learning (DL) algorithm to enable a fully automatic segmentation of the abdominal vascular tree. Methods: We proposed an algorithm based on the hybridization of a data-driven convolutional neural network and a knowledge-based model dedicated to vascular system segmentation. By using two distinct datasets of CTA from patients to evaluate independence to training dataset, the accuracy of the hybrid method for lumen and thrombus segmentation was evaluated compared to the feature-based expert system alone and to the ground truth provided by a human expert. Results: The hybrid approach demonstrated a better accuracy for lumen segmentation compared to the expert system alone (volume similarity: 0.8128 vs. 0.7912, p = 0.0006 and Dice similarity coefficient: 0.8266 vs. 0.7942, p < 0.0001). The accuracy for thrombus segmentation was also enhanced using the hybrid approach (volume similarity: 0.9404 vs. 0.9185, p = 0.0027 and Dice similarity coefficient: 0.8918 vs. 0.8654, p < 0.0001). Conclusions: By enabling a robust and fully automatic segmentation, the method could be used to develop real-time decision support to help in the management of vascular diseases.