In order to avoid the ″fragmented″ situation for complex system designed in the reliability, maintainability, testability and safety, the four qualities integration evaluation for complex system based on the color Petri net is established after determining each quality parameter. In the JAVA environment, the structure color Petrinet model and the comprehensive evaluated color Petrinet model are built using the PIPE, which turns out the four qualities integration evaluation model. When the transition is triggered, the four states of the complex system will be divided into three categories and dyed respectively. The situation of every targets and conditions are determined by the token color in place. The iteration assessments for complex system are repeated to track the four qualities status constantly and achieve the four qualities integration comprehensive design.