In the 18th century, Xu Lingtai (徐靈胎) and Yoshimasu Todo (吉益東洞) were famous doctors advocating ancient medicine, though they lived in different countries, China and Japan. We compared their major books, analyzed their academic thoughts and then took conclusions as below. 1. The first, for instance "Classified Prescriptions of Treatise on Cold Damage Diseases, 傷寒論類方" and "Classified Assemblage of Prescriptions, 類聚方". Based on essential thought that a prescription and a syndrome should correspond, these books arranged and classified the Zhang Zhongjing (張仲景)'s texts."Classified Prescriptions of Treatise on Cold Damage Diseases", based on the thought that principles, methods, formulas and medicinals (理法方藥) were integrated in prescriptions, tried to find out the implicit treatment rules in prescriptions and syndromes through analyzing "Treatise on Cold Damage Diseases, 傷寒論". On the other hand, because Classified Assemblage of Prescriptions focused on the syndromes of ancient prescriptions (古方), it classified and collected the related texts of Treatise on Cold Damage Diseases and "Synopsis of Prescriptions of the Golden Chamber, 금궤요략", and then suggested only simple instructions on how to prescribe medicine. So in this book, the trend of experience was clear. 2. The second, there is "100 Kinds Records from Shennong's Classic of Materia Medica, 神農本草經百種錄" and "Description work of herbal pharmacology comprised of excerpts from Shanhanlun and medical experiences, 藥徵". Though both of these books are professional oriental pharmacology publications that advocate reactionism, there were remarkable differences in writing style between them. "Description work of herbal pharmacology comprised of excerpts from Shanhanlun and medical experiences" was based on "Treat on Cold Damage Diseases" and "Synopsis of Prescriptions of the Golden Chamber", just explained the effects of medications and discussed 'matter of course (所當然)', but not discussed 'the reason why (所以然)'. In explaining style of syndromes, it confirmed through research, and emphasized the inductive method. On the other hand, "100 Kinds Records from Shennong's Classic of Materia Medica based on "Shennong's Classic of Materia Medica, 神農本草經", explained the nature of medications and discussed 'the reason why (所以然)'. In explaining style of syndromes, it annotated and explained, and emphasized the process of reasoning. 3. The third, there is "Discuss the Headwaters of Medicine, 醫學源流論" and Severance of Medical evils, 醫斷". Aiming the then medical theories fallen in confused state, these books brought order out of chaos, clarified the categories of medical research, and emphasized the scientific method that could put theories into practice and verify them. The difference is that "Severance of Medical Evils" researched only macroscopic viewable clinical phenomena, and even denied the existence of names of diseases and etiological causes. Thus, it emphasized the accumulation of experiences, laid emphasis on "watching and realizing (目認)", and "understand and taking in (解悟)". Discuss the Headwaters of Medicine extremely emphasized the research of 'something not occuring (未然)', that is to say, induced notions of a disease from observing clinical phenomena, furthermore based on these, predicted the 'something not occuring (未然)' and emphasized researching 'the reason why (所以然)'. As regards how they deal with the traditional theories and post-Zhang Zhongjing's medicines, "Severance of Medical evils" took completely denying attitudes. In case of "Discuss the Headwaters of Medicine", it could be used reasonably through specific situation and detailed analysis. Collectively speaking, there were some differences between medical theories of Xu Lingtai and Yoshimasu Todo. Actually, these differences were whether he tried to research the essence of disease, whether he tried to consider it rationally, and how he treated various opinions occurring in the theories of traditional medicine and clinical experience.