The training of students with high quality, responsibility and innovation capability is indentified as essential goal in college education, which also has been inevitable requirement of “Double-First Class” initiative for all universities. Civil engineering has a unique position and important roles in the training of university education. It is quite necessary not only paying attentions on process, but also on purpose of college engineering education. The inquiry-based education model has the absoluteSsuperiority because of its capability of combining process and goals together. Taking an inquiry-based teaching system with 3+2 goals has been proposed in this paper according to the basic principles of inquiry science teaching, the characteristics of engineering education and the requirements of training goals. This system includes training goals and processes of knowledge, skills, scientific approaches and study attitude. Meanwhile, a teaching strategy which is creating learning situations, posing research questions and projects has been proposed and implemented during teaching. The practice shows that this teaching mode has good efficiency on improving the innovation ability and scientific literacy of students with its strong feasibility and prominent scientificity and innovation.