The trustworthiness of Multimodal Large Language Models (MLLMs) remains an intense concern despite the significant progress in their capabilities. Existing evaluation and mitigation approaches often focus on narrow aspects and overlook risks introduced by the multimodality. To tackle these challenges, we propose MultiTrust-X, a comprehensive benchmark for evaluating, analyzing, and mitigating the trustworthiness issues of MLLMs. We define a three-dimensional framework, encompassing five trustworthiness aspects which include truthfulness, robustness, safety, fairness, and privacy; two novel risk types covering multimodal risks and cross-modal impacts; and various mitigation strategies from the perspectives of data, model architecture, training, and inference algorithms. Based on the taxonomy, MultiTrust-X includes 32 tasks and 28 curated datasets, enabling holistic evaluations over 30 open-source and proprietary MLLMs and in-depth analysis with 8 representative mitigation methods. Our extensive experiments reveal significant vulnerabilities in current models, including a gap between trustworthiness and general capabilities, as well as the amplification of potential risks in base LLMs by both multimodal training and inference. Moreover, our controlled analysis uncovers key limitations in existing mitigation strategies that, while some methods yield improvements in specific aspects, few effectively address overall trustworthiness, and many introduce unexpected trade-offs that compromise model utility. These findings also provide practical insights for future improvements, such as the benefits of reasoning to better balance safety and performance. Based on these insights, we introduce a Reasoning-Enhanced Safety Alignment (RESA) approach that equips the model with chain-of-thought reasoning ability to discover the underlying risks, achieving state-of-the-art results.