清代御藥房設立於順治十年（1653），最初隸屬太醫院，但在康熙三十年（1691）改歸內務府管轄，成為皇家私有單位。此後，御藥房在人員配置、人員升遷途徑、人員名稱與出缺性質方面幾經變化，至光緒朝中葉方底定，不再更動。就藥材來源而言，御藥房每日所需藥味，基本上是發票向太醫院委官處傳取。惟實際修合各類成藥時，御藥房所需的藥料與配料並非存放於單一地方，而是分散在各處，由御藥房依據內務府各機構職掌，分別從掌儀司、武英殿等各單位取得。就職掌而論，御藥房的工作種類繁多，其中又以加工生藥、修合各種藥料、烹調御藥以及攜藥扈從帝后出宮等最為重要，稍一不慎，即很有可能讓皇室成員的生命受到威脅。滿洲統治者僅放心將掌握皇室用藥且與皇族身家性命直接相關的御藥房，交予自己較為信任的旗人負責。內務府取得藥材較為方便以及旗人較受滿洲統治者信任，正是清廷將御藥房從太醫院改隸內務府皇家私有單位的主要原因。就御藥房與太醫院及其他各宮藥房之間的關係來看，御藥房與太醫院各有職掌，各司其責，一方面相互合作，另一方面又互相制衡。至於其他各宮藥房，大都不設首領，而是直接受御藥房管轄，唯獨慈禧太后的長春宮壽藥房例外。上述種種顯示作為制度與機構的清代御藥房，有其獨特的複雜性與多重性，實有別於明代御藥房。儘管清代御藥房係仿明制而來，且無論在人員配置或是職掌方面皆與明代御藥房有不少相似之處；然而，在「清承明制」的大架構之下，清代御藥房仍然保有許多自己的民族特色。這顯示在與漢人醫藥機構磨合的過程中，清代御藥房既部分採借漢人制度，亦部分維持滿洲民族色彩。這也說明探討清代醫療機構的建置，除了從「清承明制」的角度予以詮釋外，尚須注意滿洲人在接受明代醫療制度時，與其採用六部、內閣等中央行政制度一樣，僅為部分的、有選擇性的吸收與承襲；在此同時，仍然保持了滿洲民族的特殊性。

The Imperial Pharmacy of the Qing Dynasty was established at 1658 as subordinate units of the Imperial Medical Bureau. It was transferred to the Imperial Household Department in 1691 and since then it only serves the Imperial house. The Imperial Pharmacy did experienced several institutional change from time to time until Guanxu dynasty. The Imperial Pharmacy are responsible for all kind of pharmaceutical works included manufacture, modification, cooking and serve medicines to members of the imperial house in case of needed. This is a matter of life and death for the Imperial house of the Qing Dynasty. Therefore the Imperial Pharmacy are being supervised by trusted Bannerman assigned by the ruler. On the sources of herbs, the Imperial Pharmacy receives its herbs from the Imperial Medical Bureau. And the Imperial Pharmacy are not just stored its materials in single place but in multiple location. On the relationship between the Imperial Pharmacy, the Imperial Medical Bureau and other Pharmacy in each palace, they all have their own respective duty. And they do cooperate and balance between each other in the function. Most palace’s pharmacy don't have its supervisor but under direct supervision of the Imperial Pharmacy. All of the above shows that the Imperial Pharmacy of the Qing Dynasty has its own unique complexity and multiplicity. The institution of the Imperial Pharmacy of the Qing Dynasty is similar to the Ming Dynasty one. Even though, the Imperial Pharmacy of the Qing Dynasty still holds its ethnic characteristic feature. This implies in the process of mixture with Han Chinese medical institution, the Imperial Pharmacy of Qing Dynasty not only learn from Han Chinese but also to keep their ethnic tradition. This did tell us “Qing Cheng Ming” cannot be applying to the Medical institution of the Qing Dynasty without any reconsideration. In fact, when Manchus accepted the Medical System of the Ming Dynasty, they still partially keep their ethnic characteristic. It shows that in the discussions about the establishment of medical institution in the Qing Dynasty we should not only to illustrate it from “Qing Cheng Ming” but also the selective acceptance of Ming medical system just like all other bureaucratic system to keep their ethnic characteristic.