There are some problems in structure design with PKPM CAD software, such as the input of beams and the load verification on beams, the calculation of crack width, the calculation of internal forces and the disposition of reinforced bars of the special-shaped columns, the loads transfer of the complex structure with wall-supported-by-girder and the cantilever beams on the supported walls and etc. In the processes of design and analysis, the calculation results of this software should be adjusted. Based on engineering practice and theoretical analysis, the causes of these problems have been studied and the corresponding solutions have been introduced.