The civil engineering graduation design is a special comprehensive training that combines professional theory and engineering practice with many tasks. According to the practical teaching characteristics of civil engineering graduation design, the paper puts forward some countermeasures on how to carry out online guidance effectively under the COVID-19 epidemic to ensure the progress and quality. This paper analyzes the difficulties of online guidance of civil engineering graduation design such as difficulty in finding professional design manuals and specifications, poor intuitiveness in drawing guidance and theoretical derivation, poor individual learning atmosphere and difficulty in supervision by teachers. The paper probes into the countermeasures from the aspects of constructing electronic literature database, using multi-dimensional network teaching platform, enhancing interactive activities, refining task objectives, strengthening process management, and controlling and guaranteeing design quality and progress. Combining with concrete cases, the paper introduces the implementation process and teaching effect, and forms a set of effective online guidance mode which gives prominence to the principal position of students and the leading role of teachers. It achieves the expected teaching goal and effect which can be used for reference in online instruction of the same kind of design courses.