The multi-dimensional connotations of “autonomy” within China’s independent knowledge system of area studies are manifested in various aspects during the process of discipline construction, including academic subjectivity, independence of research paradigms, and the indigenous nature of value orientations. In terms of knowledge production, such autonomy is reflected in the integration of localization and internationalization, independent knowledge innovation, and the dissemination of autonomous knowledge. The significance of the discipline’s development lies in its contributions to enhancing the country’s soft power, serving national strategic needs, and promoting disciplinary growth and international exchanges. Faced with challenges such as the influence of Western theories, obstacles to interdisciplinary integration, and competition for international discourse power, strategies to address these issues include strengthening academic self-confidence, promoting interdisciplinary integration, and actively participating in international academic exchanges. The fundamental components of the independent knowledge system of area studies should encompass comprehensive regional knowledge, specialized country-specific knowledge, research methodologies for area studies, and a theoretical framework for area studies. These components not only serve as the cognitive foundation for constructing and facilitating the high-quality development of China’s area studies with Chinese characteristics, style, and demeanor but also provide theoretical references and practical insights for the construction of China’s independent knowledge system.