Innovative thinking competence is one of five requirements of "21st century competence level." E-Learning is a new and significant branch of education, and the paper makes a research on discovering an effective method of cultivating students' innovation under the E-Learning pattern, combining the teaching character of the course of auto control principle, and concludes that we should carry out the student-centered teaching method, take cultivation of studentspsila innovative thinking competence as a core, and bring the modern technology of education into teaching in classrooms. Teaching practice demonstrates that E-Learning teaching pattern effectively stimulates studentspsila interesting in study, cultivate the studentspsila innovative thinking competence, and improve the teaching quality.