Electronic unit pump (EUP) can satisfy both diesel engine emission legislation and fuel economy by improving injection pressure and numerical control. Fluctuations in cycle fuel injection quantity (CFIQ) of EUP determine the coherence and stability of the EUP fuel injection system. The EUP simulation model is developed in the AMESim environment. The method for the simulation experiment is designed in the MODDE environment using the design of experiments method. The results of the simulation reveal the variation laws of correlation between parameters with interaction or no interaction under overall operating conditions of diesel engines. In addition, the results also show the EUP system is a complex nonlinear system. Under overall operating conditions, all the characteristic parameters, such as fuel supply pressure, cam profile velocity, control valve lift, injector opening pressure, injector needle lift, and injector flow coefficient, have significant correlation with CFIQ. The interacting first-order factors exhibit the most significant correlation with CFIQ. The self-interacting second-order factors have significant secondary correlation with CFIQ.