Zhu Zhenheng, the last generation and sole representative from Southern China among the four masters of Jin-Yuan medicine, synthesized the evolution of Chinese medicine from the Song to the Yuan dynasties, profoundly impacting East Asian medical history. Zhu, identified as a Neo-Confucian scholar, appears in the <i>Scholarly Records of the Song-Yuan Dynasties</i> and in ‘the Biographies of Confucians’ rather than ‘the Biographies of Experts’ in the <i>Official History of the Yuan Dynasty</i>. His close association with the Jinhua school of Daoxue is noteworthy. Zhu’s career, as well as his medical theory and practice, exemplify the influence of Zhu Xi’s Neo-Confucianism, which was a significant intellectual resource among the literati during the late Yuan period, on medicine. Zhu Zhenheng’s model of a Confucian physician later became a paradigm in East Asia, as Neo-Confucianism gained mainstream acceptance among the literati. This paper offers a detailed exploration of the specific contexts of Zhu’s social and intellectual networks as well as an examination of the characteristics of his medical theories and practices. It explores how Zhu’s career and identity as a Neo-Confucian physician were shaped through the local and empire-wide networks of the Jinhua school of Neo-Confucianism within the broader context of the Mongol empire, a global power in the late Yuan period. The paper also examines in depth how Zhu’s medical practices were influenced by Neo-Confucianism, and it investigates the real nature and significance of the integration of medicine and Neo-Confucianism, two distinctly different realms of knowledge. Zhu Zhenheng’s medical theories were formed through concerns about <i>jufang</i> medicine and the active presentation of alternatives. A notable aspect of his integration of medicine and Confucianism was the adoption of Neo-Confucian terminologies, concepts, and philosophical and ethical theses, while ensuring that the unique and independent domain of medicine was not subordinated to abstract philosophical theories. This is especially evident through his active and effective use of medical cases. Unlike previous studies, this paper demonstrates that Zhu Zhenheng’s integration of medicine and Neo-Confucianism was mostly a metalevel process, involving methodology and knowledge reproduction patterns, and was driven by a belief in the possibility of harmonizing with Daoxue’s ultimate principle without undermining the autonomy of medical knowledge.