The pharmacy management of medical institutions is the basic condition for the pharmacy management of medical alliances. There are many common factors in the pharmacy management of each medical institution, and these common factors are the basic conditions for the pharmacy management of medical alliances. The pharmacy management of a medical alliance is composed of both shared aspects and aspects that meet the individual needs of different medical institutions. There are many problems in the primary medical institutions of the medical alliances, such as obsolete concepts of pharmacy management and weak pharmaceutical service capabilities. Pharmaceutical information collection is an important part in the pharmacy management of medical institutions, which can connect all aspects and better reflect the advantages of the special organization of the medical alliances. This paper explores pharmacy management in medical consortia for the specific organisational form of medical alliances, examines the basic situation of pharmacy management in different medical institutions in medical consortia, analyzes the basic conditions and basic characteristics of pharmacy management in medical consortia, so as to find a breakthrough in pharmacy management in medical consortia.