Safety is the core of the quality of Chinese materia medica products， and microbial pollution caused by medicinal materials， decoction pieces， intermediate products and others can bring certain impact on the quality and safety of Chinese materia medica products. The reasons for this are not only the problems of medicinal materials themselves， but also the exogenous pollution introduced in the production process. How to effectively use microbial detection technology and establish an appropriate microbial quality control strategy in the whole process of Chinese materia medica production is of great significance to improve the quality of Chinese materia medica products. Therefore， the authors put forward a microbial quality control strategy in the whole process of Chinese materia medica production based on the guidance of quality by design （QbD） concept， emphasizing the scientific linkage between the internal and external microbial quality control systems to jointly ensure the quality of products in all aspects. Among them， the internal microbial quality control system includes the control of the whole chain of Chinese materia medica-decoction pieces-intermediate products-excipitents-packaging materials-final products， which should be carried out by stages and characteristics， while the external microbial quality control system includes the control of personnel-equipment and facilities-pharmaceutical water-environment， emphasizing the principle of quality risk management and the development of monitoring programs， aiming to closely integrate microbial quality risk management with the production process of Chinese materia medica products， and to classify and develop microbial control strategies in order to minimize the impact of contaminating microorganisms and effectively guarantee the quality of Chinese materia medica products.