The paper introduces the development history and status quo of the computer basic curriculum system, analyzes problems existing in the education of computer basic curriculum system in TCM colleges and universities. Based on the practices of Hunan University of Chinese Medicine, it expounds on the structuring of the computer basic curriculum system that is "general, specialized and interdisciplinary" from three aspects of major, knowledge and curriculum as well as the two categories, and points out that it is conducive to the training of students' computational thinking, innovative thinking and comprehensive capability.