Aiming at the reform demand of practical teaching in civil engineering, the teaching idea and course construction scheme of the whole course design of geotechnical engineering are put forward. The whole process of course design includes four modules, namely investigation of geotechnical engineering, excavation engineering, ground treatment, and pile foundation design. Meanwhile, the university-industry cooperation combined with practical project was established, and a comprehensive evaluation system of innovative and practical ability was built. Through the training of whole teaching process, the undergraduates can develop their skills of computing, analyzing and designing for typical geotechnical cases, improve the ability to apply knowledge wisely, and acquire the capability of design philosophy expression, communication, and corporation. Practice teaching has proved that the whole course design has achieved good results in the teaching process of course design, during which the students' learning and practice ability were improved.