Rare diseases have emerged as a critical issue in the field of global public health. Their low prevalence, high complexity, and frequent onset in childhood pose unique ethical challenges to the informed consent process in clinical trials involving pediatric patients. Although clinical trials offer potential therapeutic hope for children with rare diseases, the ethical tension between proxy consent and the child's own assent further complicates the informed consent procedure. Moreover, the presence of "therapeutic misconception" undermines the autonomous decision-making capacity of both the child and their proxies, potentially violating the principles of beneficence and non-maleficence. In response to these challenges, this paper proposes several improvements, including multidimensional assessment and a phased, dynamic informed consent process, with the aim of optimizing informed consent procedures in clinical trials for pediatric rare diseases. These recommendations provide a theoretical foundation for enhancing informed consent practices in this field and may serve as a reference for future research in ethics.