The cultivation of undergraduate innovation ability is an important content of the cultivation of undergraduate talents in the “double first-class” construction. Synthetic biology is a new field of cross-disciplinary biology, which is praised as one of the ten new technology fields that can change the world. It is an important content of synthetic biology to construct high version classis microbial cells and to use chassis cells to synthesize cell factories. With the goal of cultivating innovative undergraduates, we integrate synthetic biology chassis microbial cell technology into the talent cultivation process. By organizing students to participate in International Genetically Engineered Machine Competition, to preside over Undergraduate Innovation and Entrepreneurship projects and to complete undergraduate graduation design projects, the students’ ability of linking theory with practice and innovation ability is improved. Moreover, as chassis microbial cell is a kind of cell whose genome has been simplified or optimized or its gene pathway has been changed, its application also brings certain biosafety risks. We standardize biosafety of chassis microbial cells by a serial of measures including bringing safety education into the training syllabus and teaching plan, publishing professional textbooks related with laboratory safety and operation procedures, developing virtual simulation experiment projects, setting up the lab access system and the information management system, and carrying out biosafety education on chassis microbial cells from purchase, management, standardized use and waste disposal. These practices provide a powerful way and effective guarantee for cultivating innovative undergraduates, and also provide support for the development of synthetic biology and cultivate new forces.