Explaining the hidden representations of Large Language Models (LLMs) is a perspective to understand LLMs' underlying inference logic and improve their reliability in application scenarios. However, previous methods introduce external ''black-box'' modules to explain ''black-box'' LLMs, increasing the potential uncertainty and failing to provide faithful explanations. In this paper, we propose a self-explaining method SEER, enhancing LLMs' explainability by aggregating the same concept and disentangling the different concepts in the representation space. In this way, SEER provides faithful explanations carried by representations synchronously with the LLMs' output. Additionally, we showcase the applications of SEER on trustworthiness-related tasks (e.g., the safety risks classification and detoxification tasks), where self-explained LLMs achieve consistent improvement in explainability and performance. More crucially, we theoretically analyze the improvement of SEER on LLMs' generalization ability through optimal transport theory.