A system for establishing a junction trace of an assembly includes a surface model creating module, a processing module, and a material inspection module. The assembly includes a first part and a second part assembled with each other. The surface model creating module scans the first part and the second part to separately establish first surface model data and second surface model data. The processing module establishes assembled surface model data according to the first surface model data and the second surface model data, determines a junction region from the assembled surface model data, and determines inspection points mapped on the assembly according to the junction region. The material inspection module inspects materials of the assembly at the inspection points. The processing module establishes a junction trace of the first part and the second part in the assembly according to a material inspection result.