The best estimation process of AP1000 Nuclear Power Plant (NPP) requires proper selections of parameters and models so as to obtain the most accurate results compared with the actual design parameters. Therefore, it is necessary to identify and evaluate the influences of these parameters and modeling approaches quantitatively and qualitatively. Based on the best estimate thermalhydraulic system code RELAP5/MOD3.2, sensitivity analysis has been performed on core partition methods, parameters, and model selections in AP1000 Nuclear Power Plant, like the core channel number, pressurizer node number, feedwater temperature, and so forth. The results show that core channel number, core channel node number, and the pressurizer node number have apparent influences on the coolant temperature variation and pressure drop through the reactor. The feedwater temperature is a sensitive factor to the Steam Generator (SG) outlet temperature and the Steam Generator outlet pressure. In addition, the cross-flow model nearly has no effects on the coolant temperature variation and pressure drop in the reactor, in both the steady state and the loss of power transient. Furthermore, some fittest parameters with which the most accurate results could be obtained have been put forward for the nuclear system simulation.