The lifespan of core graphite under neutron irradiation in a commercial molten salt reactor (MSR) has an important influence on its economy. Flattening the fast neutron flux (≥0.05 MeV) distribution in the core is the main method to extend the graphite irradiation lifespan. In this paper, the effects of the key parameters of MSRs on fast neutron flux distribution, including volume fraction (VF) of fuel salt, pitch of hexagonal fuel assembly, core zoning, and layout of control rod assemblies, were studied. The fast neutron flux distribution in a regular hexagon fuel assembly was first analyzed by varying VF and pitch. It was demonstrated that changing VF is more effective in reducing the fast neutron flux in both global and local graphite blocks. Flattening the fast neutron flux distribution of a commercial MSR core was then carried out by zoning the core into two regions under different VFs. Considering both the fast neutron flux distribution and burnup depth, an optimized core was obtained. The fast neutron flux distribution of the optimized core was further flattened by the rational arrangement of control rod channels. The calculation results show that the final optimized core could reduce the maximum fast neutron flux of the graphite blocks by about 30% and result in a more negative temperature reactivity coefficient, while slightly decreasing the burnup and maintaining a fully acceptable core temperature distribution.