Investigator-initiated clinical trials （IITs）， rarely driven by commercial interests， possess flexible research scales and prominent scientific independence and innovativeness， thereby developing rapidly in recent years. Nevertheless， compared with drug clinical trials， IIT programs face numerous issues and dilemmas in practice， particularly the conflict between the independence and frontier nature of clinical research and the protection of research subjects’ rights and interests， thus requiring further legal involvement and regulation. The promulgation of the Measures for the Administration of Investigator-Initiated Clinical Trials Conducted by Medical and Health Institutions in 2024 marks a significant step forward in the legal regulation of IIT research， yet many problems remain to be solved. On this basis， this paper conducted an in-depth analysis of several prominent and urgent legal issues in the implementation of IIT. It argued that IITs faced institutional obstacles and practical difficulties in multiple aspects， such as the development of the regulatory system， the implementation of the scientific review system， the compliance with ethical review， and the regulation of specific types of IIT projects （e.g.， off-label drug use and unapproved drugs）. Accordingly， the following suggestions were proposed， including further improving the regulatory system， implementing and optimizing the institutional construction of the scientific review system， ensuring the funding guarantee and review of IIT projects， strengthening informed consent and privacy protection， and exploring compliance paths for IIT research involving off-label drug use and unapproved drugs.