Composite and internationalized talents with a large-scale engineering perspective have become the target requirement for graduate education in civil engineering. This paper aims to explore a cross-disciplinary education system for graduate students in civil engineering. Taking the graduate education program in civil engineering at Chongqing University as an example, through target requirement analysis, a favorable multi-disciplinary integration environment for graduate education is constructed, and a cross-disciplinary education system for graduate students in civil engineering is established based on empowering civil engineering with wisdom and cross-disciplinary integration. Through more than ten years of reform and practice, innovative concepts, modes, and systems are developed, and outstanding achievements are made in talent cultivation quality, cultivation capacity, and teaching reform. Empowering civil engineering with wisdom and innovating construction assistance effectively promote the innovative ability and international perspective of graduate students in civil engineering, the composite development of graduate education from traditional civil engineering to smart construction has been achieved, and a new direction for the education reform of civil engineering graduate students has been opened up.