Particle size and morphological/shape properties ensure the reliable and sustainable use of all aggregate skeleton materials placed as constructed layers in transportation applications. The composition and packing of these aggregate assemblies rely heavily on particle size and morphological properties, which affect layer strength, modulus, and deformation response under vehicular loading and therefore facilitate the quality assurance/quality control (QA/QC) process. Aggregate imaging systems developed to date for size and shape characterization, however, have primarily focused on measurement of separated or slightly contacting aggregate particles. Development of efficient computer vision algorithms is urgently needed for image-based evaluations of densely stacked (or stockpile) aggregates, which requires image segmentation of a stockpile for the size and morphological properties of individual particles. This paper presents an innovative approach for automated segmentation and morphological analyses of stockpile aggregate images based on deep learning techniques. A task-specific stockpile aggregate image dataset is established from images collected from various quarries in Illinois. Individual particles from the stockpile images are manually labeled on each image associated with particle locations and regions. A state-of-the-art object detection and segmentation framework called Mask R-CNN is then used to train the image segmentation kernel, which enables user-independent segmentation of stockpile aggregate images. The segmentation results show good agreement with ground-truth labeling and improve the efficiency of size and morphological analyses conducted on densely stacked and overlapping particle images. Based on the presented approach, stockpile aggregate image analysis promises to become an efficient and innovative application for field-scale and in-place evaluations of aggregate materials.