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 based on empowering civil engineering with wisdom and innovating construction assistance. 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 was constructed, and a cross-disciplinary education system for graduate students in civil engineering was 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 for graduate education were developed, and outstanding achievements were made in talent cultivation quality, cultivation capacity, and teaching reform. It shows that empowering civil engineering with wisdom and innovating construction assistance effectively promotes the innovative ability and international perspective of graduate students in civil engineering, achieves the composite development of graduate education from traditional civil engineering to smart construction, and opens up a new direction for the education reform of smart civil engineering construction graduate students.