The training of students with high quality, responsibility and innovation capability is indentified as essential goal in higher education, which also is inevitable requirement of Double-First Class initiative. Civil engineering has a unique position and important roles in the training and education. It is quite necessary not only paying attentions on process, but also on purpose of engineering education. The inquiry-based education mode has the absolute superiority because of its capability of combining process and goals together. Taking civil engineering materials as an example, an inquiry-based teaching system with 3+2 goals is proposed 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 is 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.