Differed from the existed applications of generalized stochastic Petri net (GSPN) theory in machine-tool manufacturing system, reliability computation of FMS, testability parameters determination and fault analysis, a new idea of applying GSPN to model and performance analysis for the serial and parallel production system is proposed. And one typical discrete event dynamic system (DEDS), ter-unit of palletizing system, is taken as a real case to research. Based upon the established GSPN models, the working performances of serial and parallel layout are compared. Furthermore, their differences of working mechanisms including feeding mechanism, coordinating mechanism and monitoring mechanism are discussed. Thus the theoretical basis which is helpful to appraise layout plan and its reasonableness is provided. Meanwhile, the research results show that parallel layout is more advantageous to greatly improve the operational speed of production system than serial one.