Abstract: Organized scientific research, a common practice for universities undertaking major scientific and technological projects, is of great practical significance for enhancing a nation's comprehensive scientific and technological strength. However, influenced by its characteristics of modularization, scaling, and complexity, it faces several legal risks, including inadequate protection of researchers' rights and interests, improper use of research funds, and insufficient intellectual property protection of research achievements. Applying compliance programs to organized scientific research in universities is both a practical necessity and of significant value. Therefore, compliance programs should be introduced to effectively mitigate these legal risks. The construction of such compliance programs must adhere to the principle of fully embodying the spirit of scientists and the principle of openness and transparency. In terms of specific institutional design, efforts should focus on building an academic evaluation system aligned with the laws of talent development to safeguard the legitimate rights and interests of researchers; establishing a balanced approach to funding supervision to promote the proper use of research funds; and implementing intellectual property protection measures that integrate the proper attribution of research achievements with the reinforcement of research integrity. Only by doing so can a self-regulatory compliance culture be cultivated within organized scientific research teams in universities, thereby laying a solid foundation for its legally sound and sustainable development.