Abstract: Objective To establish the performance-based bonus allocation system by analyzing the performance assessment-related problems in current pharmacy management. Methods A performance assessment system was established in accordance to the requirements of pharmacy department.Bonus coefficient was calculated according to the performance assessment in combination with the professional nature of departments,categories and academic title of different staff,etc.Bonus allocation was calculated by the automatic bonus allocating system. Results The performance assessment linked up with income allocation system could greatly motivate the activity of staff,which was convenient for directors to run their department due to the transparency of personal income. Conclusion Performance assessment linked up with bonus allocation system is feasible in hospital pharmacy management.