Cycle fuel injection quantity fluctuation of electronic unit pump (EUP) determines the coherence and stability of the EUP fuel injection system. The simulation model of EUP was established in the AMESim environment, and the method of simulation experiment was designed by using the design of experiments (DOE) method. The result obtained by the simulation revealed the variation law of correlation under parameters interaction or not respectively in the overall operating conditions. The result shows that the EUP system is a complex nonlinear system. In the overall operating conditions the characteristic parameters such as fuel supply pressure, cam profile velocity, control valve lift, injector opening pressure, and injector needle lift as well as the injector flow coefficient have remarkable correlation with the cycle fuel injection quantity when there is no interaction between parameters. The second order factors under self interaction of parameters are the most remarkable second order factors when the interaction between parameters is considered.