The detection and segmentation of thrombi are essential for monitoring the disease progression of abdominal aortic aneurysms (AAAs) and for patient care and management. As they have inherent capabilities to learn complex features, deep convolutional neural networks (CNNs) have been recently introduced to improve thrombus detection and segmentation. However, investigations into the use of CNN methods is in the early stages and most of the existing methods are heavily concerned with the segmentation of thrombi, which only works after they have been detected. In this work, we propose a fully automated method for the whole process of the detection and segmentation of thrombi, which is based on a well-established mask region-based convolutional neural network (Mask R-CNN) framework that we improve with optimized loss functions. The combined use of complete intersection over union (CIoU) and smooth L1 loss was designed for accurate thrombus detection and then thrombus segmentation was improved with a modified focal loss. We evaluated our method against 60 clinically approved patient studies (i.e., computed tomography angiography (CTA) image volume data) by conducting 4-fold cross-validation. The results of comparisons to multiple other state-of-the-art methods suggested the superior performance of our method, which achieved the highest F1 score for thrombus detection (0.9197) and outperformed most metrics for thrombus segmentation.