In this article, we will consider several core configurations and run the core calculation with MCNP to obtain the neutrons distribution at THOR. The thermal neutron flux inside the vertical tubes (VT-B-VT-E) and the fast neutron flux in the first row facing to the boron neutron capture therapy (BNCT) facility (I3-I5) were tallied for indication. Based on these simulation results, the fuel elements were rearranged during the annual repair period in 2007. The epithermal neutron flux at the center of BNCT beam exit in air was measured again, and the results showed that the beam intensity increased by 50%. Comparing the neutron intensities both in reactor core and at the BNCT beam exit for several core configurations, the results show that the BNCT beam intensity can be increased without decreasing the neutron intensity in core.