With the implementation of the drug "zero-plus" policy，the current operation mode of hospital pharmacy has been changed from the original profit center to the cost center，becoming a hybrid department with the characteristics of medical technology，medical auxiliary and administrative departments. The new situation correctly grasps the positioning of the hospital pharmacy department in cost accounting and accounts for its costs in a scientific and reasonable manner is a problem that cannot be ignored in the full cost accounting of hospitals under the reform of payment methods. Based on Specific Guidelines for Cost Accounting of Public Institutions-Public Hospitals and Standards for Cost Accounting of Public Hospitals，it discusses the accounting of various departments under the pharmacy department according to their different attributes，so as to promote the high-quality cost accounting of public hospitals and put forward feasible schemes for further improving the system in the future.