The rapid development of brain science and cognitive science and the demand of education and teaching reform urge the development of brain-based education movement. With e-commerce teaching reform strategy as the research target, and literature analysis method, case teaching method and questionnaire as research methods, this paper constructs the teaching design pattern based on brain cognition of the course of Introduction to ECommerce on the basis of the detailed analysis of teaching principle based on brain, teaching theory related to brain and theories related to teaching design, taking the course of Introduction to E-Commerce in colleges and universities as an example. The investigation and analysis of the course implementation and teaching effect verify that the teaching design pattern of e-commerce course based on brain cognition can promote students’ interest in learning and knowledge mastery, providing a new teaching mode to be referred for e-commerce teaching reform.