Li Shizhen presented clinical symptoms, praised Zhang Yuanyuan, re identified disease symptoms, legislated rigorously, and used medication appropriately. During treatment, either traditional prescriptions are modified, new prescriptions are developed, or folk single proven formulas are often effective. Li Shizhen's academic ideas and research methods are very distinctive. Under new historical conditions, he improved ancient scientific methods based on his own practical experience and accumulated new experiences in scientific research. Li Shizhen successfully applied methods of observation and experimentation, comparison and classification, analysis and synthesis, critical inheritance, and historical verification. Observation and experimentation are the basic methods for studying this herb. Li Shizhen achieved great success by personally collecting and carefully observing drugs to obtain their true methods. Classification is an important task in scientific research, and the key to systematizing drug research lies in establishing classification standards. Li Shizhen broke the long-standing classification system of upper, middle, and lower grades in traditional Chinese medicine and established the three realms and sixteen parts classification system, making the classification system more scientific. In addition, he also established a more comprehensive classification system for treating various diseases based on Tao Hongjing's main treatment drugs classification system, and established the drug meridian classification system.