In the growing field of underwater robotics, Automated Underwater Vehicles (AUVs) are becoming more important for a range of uses, such as exploration, mapping, and inspection. This dissertation focuses on studying the main challenges of AUV auto-docking, considering a customized 3D simulated environment. The research breaks down this challenging task into two main parts: cage pose estimation and AUV control strategy. Using a mix of traditional and new methods, including fiducial-based systems, Convolutional Neural Networks (CNN), and Reinforcement Learning (RL), the study carries out experiments to check system performance and limitations. A significant aspect of this dissertation is using a 3D simulated environment to facilitate the development and testing of auto-docking algorithms for AUVs. This environment simulates crucial underwater dynamics, robotic sensors, and actuators, allowing for experimenting with different pose estimation techniques and control strategies. Additionally, the establishment of an RL-friendly 3D simulated environment stands as a relevant contribution, offering a reusable platform that not only validates the auto-docking algorithms developed in this study but also serves as a foundation for future RL-based underwater applications. In summary, the dissertation explores a range of scenarios to evaluate the efficacy of various auto-docking techniques. It initially utilizes visual servoing along with a traditional PID controller, followed by the introduction of more advanced methods like CNN-based pose estimators and Reinforcement Learning controllers. These methods are assessed both individually and in hybrid combinations to gauge their suitability and limitations for understanding the main challenges behind the AUV auto-docking.