According to the characteristics of food packaging process system design, such as complexity, advancement, safety and so on, the design flow and connotation of food packaging process system were put forward, with the basic method of complex packaging process system evaluation introduced. By taking the example of beer filling process, an evaluation model of packaging process system was established by using relevance matrix method. The evaluation index weights were calculated based on the relative importance of six evaluation indexes in the packaging process system. The optimal design plan of the beer packaging process was determined by judging the scientific and economic performance of the packaging process according to the evaluation scale given by the evaluation subject. The research of evaluation method provided a new theoretical basis for the design of complex food packaging process system.