Soybean (Glycine max (L.) Merrill) is a highly important crop widely used for food, edible oil, animal feed, and microbial fermentation products. Traditional phenotypic measurement methods are often time-consuming, labor-intensive, destructive to plants, and prone to human error. High-Throughput Phenotyping (HTP) enables precise assessment of multiple soybean phenotypic features, including morphology, physiology, diseases, pests, and agronomic traits. Artificial Intelligence (AI) is a research field dedicated to developing algorithms for multiple tasks. This review highlights the application of HTP and AI in soybean breeding programs. We discuss the challenges of implementing HTP in soybean breeding and focus on the potential and limitations of Deep Learning (DL) to support soybean breeding goals. We demonstrate the application of HTP to key soybean traits, several HTP platforms, as well as DL applications across different datasets and strategies for developing large foundation models. While integrating AI into soybean breeding programs remains a challenge, leveraging HTP data and Large Language Models (LLMs) could reshape soybean breeding.