Innovative education in the process of course teaching is the main path to cultivate creative talents. According to the characteristics of engineering geology course in civil engineering specialty, the author discussed innovative education from many aspects, including reformation of teaching material content, using heuristic teaching method, taking a variety of teaching methods, strengthening innovative thinking training in practice, training scientific research methods and using final examination and flexible variety of usual performance comprehensive assessment. While mastering the course knowledge, students were inspired to use the curriculum knowledge for analyzing engineering geological problems from various aspects, and were trained to be good at thinking and have a good habit of innovative thinking. In this way, the teaching goals of training innovative talents could be reached.