Cardiomyopeptidin is a kind of biological drug used in the perioperative period of cardiac surgery, and the main ingredient of it can help to repair myocardial damage. In the production of cardiomyopeptidin for injection, vacuum freeze drying is a key technology. However, it has to face many difficulties such as the long cycle of freeze drying process (78 h) and large deviation of quality in group which reduce the efficiency of product. Currently, the study of freeze drying process of cardiomyopeptidin for injection is rare. The experiments in this paper were conducted by a miniature freeze dryer, cutting down the cycle of freeze drying process to an ideal value (45 h) and diminishing the deviation of quality in group. At present, many key factors of freeze drying process of the cardiomyopeptidin have been investigated, the optimized freeze drying program successfully cuts down the cycle to 36 h in the pilot freeze dryer. Luckily, the research also found a new auxiliary material which could greatly improve the efficiency of freeze drying. This paper provides a new way for the research of freeze drying process of biological drugs.