In this research, I have tried to overview the diagnosis and treatment of smallpox performed by Heo Joon, a representative physician of Joseon dynasty. In order to accomplish this, I analyzed the smallpox related contents shown in the Essentials of Smallpox translated in Korean and a comprehensive medical book Treasured Mirror of Eastern Medicine, both written by Heo Joon. In examining these sources, I found out that Heo Joon used a medical method called 'Syndrome differentiation' in treating smallpox. Next, I compared the medical cases of smallpox left behind by physicians before and after Heo Joon, so as to shed light on the meaning Heo Joon's smallpox medicine has in the history of medicine. Heo Joon read the Compendium of Smallpox published by the Joseon government and medical books newly imported from Ming China, in order to write the Essentials of Smallpox. His goal was to concentrate all the knowledge related to smallpox in just one book. One aspect that was considered was that this book's target reader did not know anything about smallpox and could not read the Chinese letters. Heo Joon, to solve this problem, collected and organized the essentials of previous medical information and at the same time provided Korean translations. For Heo Joon, the main point of smallpox medicine was to discriminate the good or bad state of prognosis through the looks and colors of the smallpox, and to distinguish the lightness or heaviness of the symptoms through the concomitant symptoms. And such thoughts materialized into judging deficiency and excess, distinguishing concomitant symptoms, and discriminating similar symptoms. Not long after the Essentials of Smallpox was published, Treasured Mirror was published. As a comprehensive medical book that covered many diseases, Treasured Mirror had to have a coherent theoretical system on diagnosing diseases and treating them. What Heo Joon regarded as the most important content, namely discrimination and distinguishment of the looks and symptoms of smallpox, was included in Treasured Mirror in the name of 'Syndrome differentiation'. There are not any specific Heo Joon's medical case left today, so we do not know how much his smallpox medicine contributed to uplifting the cure rate of smallpox in reality. However, comparing the case in the Compendium of Smallpox to case recorded by later physicians such as Park Jinhee, Ryu Sang, syndrome differentiation proposed by Heo Joon was not only succeeded by physicians of later generations but also contributed greatly to the success in treating smallpox. Heo Joon did not know about the pathology, causes of the smallpox, discovered by biomedicine. Even considering this, his medical contribution is clear. Based on the visible symptoms of smallpox and medical accomplishments of the previous eras, he organized and compactly proposed the causes, progression, distinguishing concomitant symptoms, treatments for symptoms development, etc. of the smallpox. In addition, in order to overcome the limit of simple symptomatic treatment, he entitled the chapter of medical thought of analysis symptoms 'syndrome differentiation' present in the previous medical books. It was the advent of Joseon's edition of smallpox medicine based on syndrome differentiation.